From 1440906fd423b168f3f7e80ddab00f5d4855b31e Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Sat, 10 May 2025 22:50:31 +0200 Subject: [PATCH 01/33] optin --- nf_core/pipelines/create/template_features.yml | 8 ++++++++ nf_core/utils.py | 2 ++ tests/utils.py | 1 + 3 files changed, 11 insertions(+) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 04cc7cb062..c70fd3f03f 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -496,3 +496,11 @@ vscode: Adds the `.vscode` directory to the pipelinerepository. nfcore_pipelines: False custom_pipelines: True +gpu: + short_description: "Use GPU" + description: "Add GPU support to the pipeline" + help_text: | + This will add GPU support to the pipeline. It will add a `use_gpu` parameter to the pipeline. + The pipeline will be able to run on GPU-enabled compute environments. + nfcore_pipelines: False + custom_pipelines: True diff --git a/nf_core/utils.py b/nf_core/utils.py index 4d096ec3ac..4391ec8fca 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1141,6 +1141,8 @@ class NFCoreTemplateConfig(BaseModel): """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """ is_nfcore: Optional[bool] = None """ Whether the pipeline is an nf-core pipeline. """ + gpu: Optional[bool] = False + """ Whether the pipeline uses GPU. """ # convert outdir to str @field_validator("outdir") diff --git a/tests/utils.py b/tests/utils.py index bba3bc09ed..6c3926b02a 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -158,6 +158,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: is_nfcore=None, skip_features=None, outdir=None, + gpu=False, ), bump_version=None, ) From 087c2f0397e2af182b8a54e09e5cf76792bbb3b2 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Sat, 10 May 2025 20:57:59 +0000 Subject: [PATCH 02/33] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3e44818336..7cef3b0558 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -75,6 +75,7 @@ - Dev ([#3557](https://github.com/nf-core/tools/pull/3557)) - chore(deps): update python:3.12-slim docker digest to bae1a06 ([#3558](https://github.com/nf-core/tools/pull/3558)) - Update CI to test template pipelines with nf-test ([#3559](https://github.com/nf-core/tools/pull/3559)) +- Add opt-in feature `gpu` ([#3562](https://github.com/nf-core/tools/pull/3562)) ## [v3.2.1 - Pewter Pangolin Patch](https://github.com/nf-core/tools/releases/tag/3.2.1) - [2025-04-29] From 5f9a01cb7475a44b6ad04a79afa5173b5ad53e83 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Mon, 2 Jun 2025 12:40:21 +0200 Subject: [PATCH 03/33] restructured the features, add GPU and downstream sample sheet, turned off features as defaut --- nf_core/pipelines/create/custompipeline.py | 12 +- nf_core/pipelines/create/nfcorepipeline.py | 8 +- .../pipelines/create/template_features.yml | 581 ++++++++++-------- nf_core/pipelines/create/utils.py | 5 +- nf_core/utils.py | 2 - tests/utils.py | 1 - 6 files changed, 346 insertions(+), 263 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index e433db41ec..83cc303ca0 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -23,7 +23,7 @@ def compose(self) -> ComposeResult: ) ) yield Horizontal( - Switch(id="toggle_all", value=True), + Switch(id="toggle_all", value=False), Static("Toggle all features", classes="feature_title"), classes="custom_grid", ) @@ -39,9 +39,15 @@ def on_mount(self) -> None: for name, feature in self.parent.template_features_yml.items(): if feature["custom_pipelines"]: self.query_one("#features").mount( - PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name) + PipelineFeature( + feature["help_text"], + feature["short_description"], + feature["description"], + name, + feature["default"], + ) ) - self.query_one("#toggle_all", Switch).value = True + self.query_one("#toggle_all", Switch).value = False @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py index ebb9866986..9260bbbc8f 100644 --- a/nf_core/pipelines/create/nfcorepipeline.py +++ b/nf_core/pipelines/create/nfcorepipeline.py @@ -33,7 +33,13 @@ def on_mount(self) -> None: for name, feature in self.parent.template_features_yml.items(): if feature["nfcore_pipelines"]: self.query_one("#features").mount( - PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name) + PipelineFeature( + feature["help_text"], + feature["short_description"], + feature["description"], + name, + feature["default"], + ) ) @on(Button.Pressed, "#continue") diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 42622b2158..eff08d2ff7 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -1,3 +1,4 @@ +# Repository Setup github: skippable_paths: - ".github" @@ -34,6 +35,65 @@ github: - "nextflow_badge" nfcore_pipelines: False custom_pipelines: True + default: False + +github_badges: + skippable_paths: False + short_description: "Add Github badges" + description: "The README.md file of the pipeline will include GitHub badges" + help_text: | + The pipeline `README.md` will include badges for: + * AWS CI Tests + * Zenodo DOI + * Nextflow + * nf-core template version + * Conda + * Docker + * Singularity + * Launching on Nextflow Tower + linting: + readme: + - "nextflow_badge" + - "nfcore_template_badge" + nfcore_pipelines: False + custom_pipelines: True + default: False + +changelog: + skippable_paths: + - "CHANGELOG.md" + short_description: "Add a changelog" + description: "Add a CHANGELOG.md file." + help_text: | + Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. + + You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ + linting: + files_exist: + - "CHANGELOG.md" + nfcore_pipelines: False + custom_pipelines: True + default: False + +license: + skippable_paths: + - "LICENSE" + short_description: "Add a license File" + description: "Add the MIT license file." + help_text: | + To protect the copyright of the pipeline, you can add a LICENSE file. + This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT + linting: + files_exist: + - "LICENSE" + files_unchanged: + - "LICENSE" + nfcore_pipelines: False + custom_pipelines: True + default: False + +# Continuous Integration & Testing + ci: skippable_paths: - ".github/workflows/" @@ -59,6 +119,74 @@ ci: - ".github/workflows/linting.yml" nfcore_pipelines: False custom_pipelines: True + default: False + +test_config: + skippable_paths: + - "conf/test.config" + - "conf/test_full.config" + - ".github/workflows/awsfulltest.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + short_description: "Add testing profiles" + description: "Add two default testing profiles" + help_text: | + This will add two default testing profiles to run the pipeline with different inputs. + You can customise them and add other test profiles. + + These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run -profile test`. + + The pipeline will include two profiles: `test` and `test_full`. + In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario. + linting: + files_exist: + - "conf/test.config" + - "conf/test_full.config" + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + nextflow_config: False + files_unchanged: + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + nfcore_pipelines: False + custom_pipelines: True + default: False + +nf-test: + skippable_paths: + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + - "nf-test.config" + - "tests/default.nf.test" + - "tests/.nftignore" + - "tests/nextflow.config" + short_description: "Add pipeline testing" + description: "Add pipeline testing using nf-test" + help_text: | + This will add pipeline testing with [nf-test](https://www.nf-test.com/). + + Will add and `nf-test.config` file setting up the appropriate configuration to test your pipeline. + On top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests. + + If you skip this feature, you will still be able to test your pipeline with a `test` profile by running the pipeline. + But you won't have the automated CI testing. + You can add CI by yourself. + linting: + files_exist: + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + - "nf-test.config" + - "tests/default.nf.test" + nfcore_pipelines: False + custom_pipelines: True + default: False + +# Components & Modules igenomes: skippable_paths: - "conf/igenomes.config" @@ -82,26 +210,114 @@ igenomes: - "conf/igenomes_ignored.config" nfcore_pipelines: True custom_pipelines: True -github_badges: - skippable_paths: False - short_description: "Add Github badges" - description: "The README.md file of the pipeline will include GitHub badges" + default: False + +modules: + skippable_paths: + - "conf/base.config" + - "conf/modules.config" + - "modules.json" + - "modules" + - "subworkflows" + short_description: "Use nf-core components" + description: "Include all required files to use nf-core modules and subworkflows" help_text: | - The pipeline `README.md` will include badges for: - * AWS CI Tests - * Zenodo DOI - * Nextflow - * nf-core template version - * Conda - * Docker - * Singularity - * Launching on Nextflow Tower + It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline. + This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands. linting: - readme: - - "nextflow_badge" - - "nfcore_template_badge" + nfcore_components: False + modules_json: False + base_config: False + modules_config: False + files_exist: + - "conf/base.config" + - "conf/modules.config" + - "modules.json" + nfcore_pipelines: False + custom_pipelines: True + default: False + +multiqc: + skippable_paths: + - "assets/multiqc_config.yml" + - "assets/methods_description_template.yml" + - "modules/nf-core/multiqc/" + short_description: "Use multiqc" + description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." + help_text: | + MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. + + The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. + linting: + files_unchanged: + - ".github/CONTRIBUTING.md" + - "assets/sendmail_template.txt" + files_exist: + - "assets/multiqc_config.yml" + multiqc_config: False + nfcore_pipelines: True + custom_pipelines: True + default: False + +fastqc: + skippable_paths: + - "modules/nf-core/fastqc/" + short_description: "Use fastqc" + description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." + help_text: | + FastQC is a tool which provides quality control checks on raw sequencing data. + The pipeline will include the FastQC module. + nfcore_pipelines: True + custom_pipelines: True + default: False + +nf_schema: + skippable_paths: + - "subworkflows/nf-core/utils_nfschema_plugin" + - "nextflow_schema.json" + - "assets/schema_input.json" + - "assets/samplesheet.csv" + short_description: "Use nf-schema" + description: "Use the nf-schema Nextflow plugin for this pipeline." + help_text: | + [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema. + It also provides helper functionality to create help messages, get a summary + of changed parameters and validate and convert a samplesheet to a channel. + linting: + files_exist: + - "nextflow_schema.json" + schema_params: False + schema_lint: False + schema_description: False + nextflow_config: False + nfcore_pipelines: True + custom_pipelines: True + default: False + +downstream_samplesheet: + skippable_paths: + - "subworkflows/local/generate_downstream_samplesheets" + short_description: "Generate downstream samplesheets" + description: "The pipeline will include the generate_downstream_samplesheets subworkflow for the generation of a samplesheet for other downstream pipelines." + help_text: | + The pipeline will include the generate_downstream_samplesheets subworkflow. + The subworkflow generate_downstream_samplesheets provides a base template for generating samplesheets by taking a specified input channel of i.e. reads or fasta extracts its metadata for generating samplesheets. + nfcore_pipelines: True + custom_pipelines: True + default: False + +gpu: + skippable_paths: False + short_description: "Use GPU" + description: "Add GPU support to the pipeline" + help_text: | + This will add GPU support to the pipeline. It will add a `use_gpu` parameter to the pipeline. + The pipeline will be able to run on GPU-enabled compute environments. nfcore_pipelines: False custom_pipelines: True + default: False + +# Configurations nf_core_configs: skippable_paths: False short_description: "Add configuration files" @@ -127,6 +343,8 @@ nf_core_configs: included_configs: False nfcore_pipelines: False custom_pipelines: True + default: False + is_nfcore: skippable_paths: - ".github/ISSUE_TEMPLATE/config" @@ -167,44 +385,24 @@ is_nfcore: - "report_comment" nfcore_pipelines: False custom_pipelines: False -code_linters: + default: False + +seqera_platform: skippable_paths: - - ".pre-commit-config.yaml" - - ".prettierignore" - - ".prettierrc.yml" - - ".github/workflows/fix-linting.yml" - short_description: "Use code linters" - description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." + - "tower.yml" + short_description: "Add Seqera Platform output" + description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform" help_text: | - Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. - Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. - The available code linters are: + When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options. - - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. - - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). - linting: - files_exist: - - ".prettierignore" - - ".prettierrc.yml" + In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform. + You can extend this file adding any other desired configuration. nfcore_pipelines: False custom_pipelines: True -citations: - skippable_paths: - - "assets/methods_description_template.yml" - - "CITATIONS.md" - short_description: "Include citations" - description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." - help_text: | - If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. - - Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, - and the logics to add this section to the output MultiQC report (if the report is generated). - linting: - files_exist: - - "CITATIONS.md" - nfcore_pipelines: False - custom_pipelines: True -gitpod: + default: False + +# Development Environments +gitpod: skippable_paths: - ".gitpod.yml" short_description: "Include a gitpod environment" @@ -216,6 +414,8 @@ gitpod: This is useful to have all the tools ready for pipeline development. nfcore_pipelines: False custom_pipelines: True + default: False + codespaces: skippable_paths: - ".devcontainer/devcontainer.json" @@ -231,109 +431,104 @@ codespaces: - ".github/CONTRIBUTING.md" nfcore_pipelines: False custom_pipelines: True -multiqc: - skippable_paths: - - "assets/multiqc_config.yml" - - "assets/methods_description_template.yml" - - "modules/nf-core/multiqc/" - short_description: "Use multiqc" - description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." - help_text: | - MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. + default: False - The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. - linting: - files_unchanged: - - ".github/CONTRIBUTING.md" - - "assets/sendmail_template.txt" - files_exist: - - "assets/multiqc_config.yml" - multiqc_config: False - nfcore_pipelines: True - custom_pipelines: True -fastqc: +vscode: skippable_paths: - - "modules/nf-core/fastqc/" - short_description: "Use fastqc" - description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." + - ".vscode" + short_description: "Render website admonitions in VSCode" + description: "Add a VSCode configuration to render website admonitions" help_text: | - FastQC is a tool which provides quality control checks on raw sequencing data. - The pipeline will include the FastQC module. - nfcore_pipelines: True + This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website. + + Adds the `.vscode` directory to the pipelinerepository. + nfcore_pipelines: False custom_pipelines: True -modules: + default: False + +# Code Quality +code_linters: skippable_paths: - - "conf/base.config" - - "conf/modules.config" - - "modules.json" - - "modules" - - "subworkflows" - short_description: "Use nf-core components" - description: "Include all required files to use nf-core modules and subworkflows" + - ".pre-commit-config.yaml" + - ".prettierignore" + - ".prettierrc.yml" + - ".github/workflows/fix-linting.yml" + short_description: "Use code linters" + description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." help_text: | - It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline. - This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands. + Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. + Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. + The available code linters are: + + - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. + - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). linting: - nfcore_components: False - modules_json: False - base_config: False - modules_config: False files_exist: - - "conf/base.config" - - "conf/modules.config" - - "modules.json" + - ".prettierignore" + - ".prettierrc.yml" nfcore_pipelines: False custom_pipelines: True -changelog: + default: False + +# Documentation & Metadata +citations: skippable_paths: - - "CHANGELOG.md" - short_description: "Add a changelog" - description: "Add a CHANGELOG.md file." + - "assets/methods_description_template.yml" + - "CITATIONS.md" + short_description: "Include citations" + description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." help_text: | - Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. + If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. - You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ + Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, + and the logics to add this section to the output MultiQC report (if the report is generated). linting: files_exist: - - "CHANGELOG.md" + - "CITATIONS.md" nfcore_pipelines: False custom_pipelines: True -nf_schema: + default: False + +documentation: skippable_paths: - - "subworkflows/nf-core/utils_nfschema_plugin" - - "nextflow_schema.json" - - "assets/schema_input.json" - - "assets/samplesheet.csv" - short_description: "Use nf-schema" - description: "Use the nf-schema Nextflow plugin for this pipeline." + - "docs" + short_description: "Add documentation" + description: "Add documentation to the pipeline" help_text: | - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema. - It also provides helper functionality to create help messages, get a summary - of changed parameters and validate and convert a samplesheet to a channel. + This will add documentation markdown files where you can describe your pipeline. + It includes: + - docs/README.md: A README file where you can describe the structure of your documentation. + - docs/output.md: A file where you can explain the output generated by the pipeline + - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters. + + These files come with an exemplary documentation structure written. linting: files_exist: - - "nextflow_schema.json" - schema_params: False - schema_lint: False - schema_description: False - nextflow_config: False - nfcore_pipelines: True + - "docs/output.md" + - "docs/README.md" + - "docs/usage.md" + nfcore_pipelines: False custom_pipelines: True -license: + default: False + +rocrate: skippable_paths: - - "LICENSE" - short_description: "Add a license File" - description: "Add the MIT license file." + - "ro-crate-metadata.json" + short_description: "Add RO-Crate metadata" + description: "Add a RO-Crate metadata file to describe the pipeline" help_text: | - To protect the copyright of the pipeline, you can add a LICENSE file. - This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT - linting: - files_exist: - - "LICENSE" - files_unchanged: - - "LICENSE" + RO-Crate is a metadata specification to describe research data and software. + This will add a `ro-crate-metadata.json` file to describe the pipeline. nfcore_pipelines: False custom_pipelines: True + linting: + files_warn: + - "ro-crate-metadata.json" + files_unchanged: + - ".prettierignore" + default: False + +# Notifications email: skippable_paths: - "assets/email_template.html" @@ -352,6 +547,8 @@ email: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True + default: False + adaptivecard: skippable_paths: - "assets/adaptivecard.json" @@ -365,6 +562,8 @@ adaptivecard: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True + default: False + slackreport: skippable_paths: - "assets/slackreport.json" @@ -377,131 +576,5 @@ slackreport: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True -documentation: - skippable_paths: - - "docs" - short_description: "Add documentation" - description: "Add documentation to the pipeline" - help_text: | - This will add documentation markdown files where you can describe your pipeline. - It includes: - - docs/README.md: A README file where you can describe the structure of your documentation. - - docs/output.md: A file where you can explain the output generated by the pipeline - - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters. - - These files come with an exemplary documentation structure written. - linting: - files_exist: - - "docs/output.md" - - "docs/README.md" - - "docs/usage.md" - nfcore_pipelines: False - custom_pipelines: True -test_config: - skippable_paths: - - "conf/test.config" - - "conf/test_full.config" - - ".github/workflows/awsfulltest.yml" - - ".github/workflows/awstest.yml" - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - short_description: "Add testing profiles" - description: "Add two default testing profiles" - help_text: | - This will add two default testing profiles to run the pipeline with different inputs. - You can customise them and add other test profiles. - - These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run -profile test`. - - The pipeline will include two profiles: `test` and `test_full`. - In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario. - linting: - files_exist: - - "conf/test.config" - - "conf/test_full.config" - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - nextflow_config: False - files_unchanged: - - ".github/CONTRIBUTING.md" - - ".github/PULL_REQUEST_TEMPLATE.md" - nfcore_pipelines: False - custom_pipelines: True -nf-test: - skippable_paths: - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - - "nf-test.config" - - "tests/default.nf.test" - - "tests/.nftignore" - - "tests/nextflow.config" - short_description: "Add pipeline testing" - description: "Add pipeline testing using nf-test" - help_text: | - This will add pipeline testing with [nf-test](https://www.nf-test.com/). - - Will add and `nf-test.config` file setting up the appropriate configuration to test your pipeline. - On top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests. - - If you skip this feature, you will still be able to test your pipeline with a `test` profile by running the pipeline. - But you won't have the automated CI testing. - You can add CI by yourself. - linting: - files_exist: - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - - "nf-test.config" - - "tests/default.nf.test" - nf_test_content: False - nfcore_pipelines: False - custom_pipelines: True -seqera_platform: - skippable_paths: - - "tower.yml" - short_description: "Add Seqera Platform output" - description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform" - help_text: | - When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options. - - In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform. - You can extend this file adding any other desired configuration. - nfcore_pipelines: False - custom_pipelines: True -rocrate: - skippable_paths: - - "ro-crate-metadata.json" - short_description: "Add RO-Crate metadata" - description: "Add a RO-Crate metadata file to describe the pipeline" - help_text: | - RO-Crate is a metadata specification to describe research data and software. - This will add a `ro-crate-metadata.json` file to describe the pipeline. - nfcore_pipelines: False - custom_pipelines: True - linting: - files_warn: - - "ro-crate-metadata.json" - files_unchanged: - - ".prettierignore" -vscode: - skippable_paths: - - ".vscode" - short_description: "Render website admonitions in VSCode" - description: "Add a VSCode configuration to render website admonitions" - help_text: | - This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website. - - Adds the `.vscode` directory to the pipelinerepository. - nfcore_pipelines: False - custom_pipelines: True -gpu: - short_description: "Use GPU" - description: "Add GPU support to the pipeline" - help_text: | - This will add GPU support to the pipeline. It will add a `use_gpu` parameter to the pipeline. - The pipeline will be able to run on GPU-enabled compute environments. - nfcore_pipelines: False - custom_pipelines: True + default: False +# newest version bump diff --git a/nf_core/pipelines/create/utils.py b/nf_core/pipelines/create/utils.py index 7f435421a5..aef1204846 100644 --- a/nf_core/pipelines/create/utils.py +++ b/nf_core/pipelines/create/utils.py @@ -176,12 +176,13 @@ def hide(self) -> None: class PipelineFeature(Static): """Widget for the selection of pipeline features.""" - def __init__(self, markdown: str, title: str, subtitle: str, field_id: str, **kwargs) -> None: + def __init__(self, markdown: str, title: str, subtitle: str, field_id: str, default: bool, **kwargs) -> None: super().__init__(**kwargs) self.markdown = markdown self.title = title self.subtitle = subtitle self.field_id = field_id + self.default = default def on_button_pressed(self, event: Button.Pressed) -> None: """When the button is pressed, change the type of the button.""" @@ -198,7 +199,7 @@ def compose(self) -> ComposeResult: Hidden row with a help text box. """ yield HorizontalScroll( - Switch(value=True, id=self.field_id), + Switch(value=self.default, id=self.field_id), Static(self.title, classes="feature_title"), Static(self.subtitle, classes="feature_subtitle"), Button("Show help", id="show_help", variant="primary"), diff --git a/nf_core/utils.py b/nf_core/utils.py index f58391b3d0..b608c69602 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1141,8 +1141,6 @@ class NFCoreTemplateConfig(BaseModel): """ Skip features. See https://nf-co.re/docs/nf-core-tools/pipelines/create for a list of features. """ is_nfcore: Optional[bool] = None """ Whether the pipeline is an nf-core pipeline. """ - gpu: Optional[bool] = False - """ Whether the pipeline uses GPU. """ # convert outdir to str @field_validator("outdir") diff --git a/tests/utils.py b/tests/utils.py index 6c3926b02a..bba3bc09ed 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -158,7 +158,6 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: is_nfcore=None, skip_features=None, outdir=None, - gpu=False, ), bump_version=None, ) From edc124fdce37acd47b6533573d65a69cec9b2879 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Tue, 3 Jun 2025 16:42:51 +0200 Subject: [PATCH 04/33] all features are on except for gpu --- .../pipelines/create/template_features.yml | 54 +++++++++---------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index eff08d2ff7..e3dc979957 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -35,7 +35,7 @@ github: - "nextflow_badge" nfcore_pipelines: False custom_pipelines: True - default: False + default: True github_badges: skippable_paths: False @@ -57,7 +57,7 @@ github_badges: - "nfcore_template_badge" nfcore_pipelines: False custom_pipelines: True - default: False + default: True changelog: skippable_paths: @@ -73,7 +73,7 @@ changelog: - "CHANGELOG.md" nfcore_pipelines: False custom_pipelines: True - default: False + default: true license: skippable_paths: @@ -90,7 +90,7 @@ license: - "LICENSE" nfcore_pipelines: False custom_pipelines: True - default: False + default: true # Continuous Integration & Testing @@ -119,7 +119,7 @@ ci: - ".github/workflows/linting.yml" nfcore_pipelines: False custom_pipelines: True - default: False + default: true test_config: skippable_paths: @@ -153,7 +153,7 @@ test_config: - ".github/PULL_REQUEST_TEMPLATE.md" nfcore_pipelines: False custom_pipelines: True - default: False + default: true nf-test: skippable_paths: @@ -184,7 +184,7 @@ nf-test: - "tests/default.nf.test" nfcore_pipelines: False custom_pipelines: True - default: False + default: true # Components & Modules igenomes: @@ -210,7 +210,7 @@ igenomes: - "conf/igenomes_ignored.config" nfcore_pipelines: True custom_pipelines: True - default: False + default: true modules: skippable_paths: @@ -235,7 +235,7 @@ modules: - "modules.json" nfcore_pipelines: False custom_pipelines: True - default: False + default: true multiqc: skippable_paths: @@ -257,7 +257,7 @@ multiqc: multiqc_config: False nfcore_pipelines: True custom_pipelines: True - default: False + default: true fastqc: skippable_paths: @@ -269,7 +269,7 @@ fastqc: The pipeline will include the FastQC module. nfcore_pipelines: True custom_pipelines: True - default: False + default: true nf_schema: skippable_paths: @@ -292,11 +292,11 @@ nf_schema: nextflow_config: False nfcore_pipelines: True custom_pipelines: True - default: False + default: true downstream_samplesheet: skippable_paths: - - "subworkflows/local/generate_downstream_samplesheets" + - "subworkflows" short_description: "Generate downstream samplesheets" description: "The pipeline will include the generate_downstream_samplesheets subworkflow for the generation of a samplesheet for other downstream pipelines." help_text: | @@ -304,7 +304,7 @@ downstream_samplesheet: The subworkflow generate_downstream_samplesheets provides a base template for generating samplesheets by taking a specified input channel of i.e. reads or fasta extracts its metadata for generating samplesheets. nfcore_pipelines: True custom_pipelines: True - default: False + default: true gpu: skippable_paths: False @@ -343,7 +343,7 @@ nf_core_configs: included_configs: False nfcore_pipelines: False custom_pipelines: True - default: False + default: true is_nfcore: skippable_paths: @@ -385,7 +385,7 @@ is_nfcore: - "report_comment" nfcore_pipelines: False custom_pipelines: False - default: False + default: true seqera_platform: skippable_paths: @@ -399,7 +399,7 @@ seqera_platform: You can extend this file adding any other desired configuration. nfcore_pipelines: False custom_pipelines: True - default: False + default: true # Development Environments gitpod: @@ -414,7 +414,7 @@ gitpod: This is useful to have all the tools ready for pipeline development. nfcore_pipelines: False custom_pipelines: True - default: False + default: true codespaces: skippable_paths: @@ -431,7 +431,7 @@ codespaces: - ".github/CONTRIBUTING.md" nfcore_pipelines: False custom_pipelines: True - default: False + default: true vscode: skippable_paths: @@ -444,7 +444,7 @@ vscode: Adds the `.vscode` directory to the pipelinerepository. nfcore_pipelines: False custom_pipelines: True - default: False + default: true # Code Quality code_linters: @@ -468,7 +468,7 @@ code_linters: - ".prettierrc.yml" nfcore_pipelines: False custom_pipelines: True - default: False + default: true # Documentation & Metadata citations: @@ -487,7 +487,7 @@ citations: - "CITATIONS.md" nfcore_pipelines: False custom_pipelines: True - default: False + default: true documentation: skippable_paths: @@ -509,7 +509,7 @@ documentation: - "docs/usage.md" nfcore_pipelines: False custom_pipelines: True - default: False + default: true rocrate: skippable_paths: @@ -526,7 +526,7 @@ rocrate: - "ro-crate-metadata.json" files_unchanged: - ".prettierignore" - default: False + default: true # Notifications email: @@ -547,7 +547,7 @@ email: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True - default: False + default: true adaptivecard: skippable_paths: @@ -562,7 +562,7 @@ adaptivecard: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True - default: False + default: true slackreport: skippable_paths: @@ -576,5 +576,5 @@ slackreport: - ".prettierignore" nfcore_pipelines: False custom_pipelines: True - default: False + default: true # newest version bump From e33055bdc14ae500b00bfd9e1afaa9ece072a9ab Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Fri, 6 Jun 2025 16:27:36 +0200 Subject: [PATCH 05/33] update snapshot --- .../pipelines/create/template_features.yml | 2 +- .../test_customisation_help.svg | 257 +++++++++--------- .../test_create_app/test_type_custom.svg | 256 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 251 ++++++++--------- .../test_type_nfcore_validation.svg | 252 ++++++++--------- 5 files changed, 510 insertions(+), 508 deletions(-) diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index e3dc979957..dbb694cb00 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -302,7 +302,7 @@ downstream_samplesheet: help_text: | The pipeline will include the generate_downstream_samplesheets subworkflow. The subworkflow generate_downstream_samplesheets provides a base template for generating samplesheets by taking a specified input channel of i.e. reads or fasta extracts its metadata for generating samplesheets. - nfcore_pipelines: True + nfcore_pipelines: False custom_pipelines: True default: true diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 9ded670d60..4c0475979a 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,257 +19,256 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1435926941-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1435926941-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #94999c } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #191919 } -.terminal-r7 { fill: #1e1e1e } -.terminal-r8 { fill: #6db2ff } -.terminal-r9 { fill: #808080 } -.terminal-r10 { fill: #ddedf9;font-weight: bold } -.terminal-r11 { fill: #004295 } -.terminal-r12 { fill: #000000 } -.terminal-r13 { fill: #0178d4 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #272727 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0d0d0d } -.terminal-r18 { fill: #333333 } -.terminal-r19 { fill: #7ae998 } -.terminal-r20 { fill: #0a180e;font-weight: bold } -.terminal-r21 { fill: #008139 } -.terminal-r22 { fill: #ffa62b;font-weight: bold } -.terminal-r23 { fill: #495259 } + .terminal-1435926941-r1 { fill: #c5c8c6 } +.terminal-1435926941-r2 { fill: #e3e3e3 } +.terminal-1435926941-r3 { fill: #989898 } +.terminal-1435926941-r4 { fill: #e1e1e1 } +.terminal-1435926941-r5 { fill: #4ebf71;font-weight: bold } +.terminal-1435926941-r6 { fill: #1e1e1e } +.terminal-1435926941-r7 { fill: #e2e2e2 } +.terminal-1435926941-r8 { fill: #507bb3 } +.terminal-1435926941-r9 { fill: #808080 } +.terminal-1435926941-r10 { fill: #dde6ed;font-weight: bold } +.terminal-1435926941-r11 { fill: #001541 } +.terminal-1435926941-r12 { fill: #14191f } +.terminal-1435926941-r13 { fill: #0178d4 } +.terminal-1435926941-r14 { fill: #454a50 } +.terminal-1435926941-r15 { fill: #e2e3e3;font-weight: bold } +.terminal-1435926941-r16 { fill: #000000 } +.terminal-1435926941-r17 { fill: #7ae998 } +.terminal-1435926941-r18 { fill: #0a180e;font-weight: bold } +.terminal-1435926941-r19 { fill: #008139 } +.terminal-1435926941-r20 { fill: #fea62b;font-weight: bold } +.terminal-1435926941-r21 { fill: #a7a9ab } +.terminal-1435926941-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous ▂▂ -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be  Hide help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common  -reference genome files  -from iGenomes - - -Nf-core pipelines are configured to use a copy of the most common reference  -genome files. - -By selecting this option, your pipeline will include a configuration file  -specifying the paths to these files. - -The required code to use these files will also be included in the template. When -the pipeline user provides an appropriate genome key, the pipeline will  -automatically download the required reference files. -▅▅ -For more information about reference genomes in nf-core pipelines, see the  - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎        Toggle all features +▊▁▁▁▁▁▁▁▁▎ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▄▄ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a changelogAdd a CHANGELOG.md  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add testing profilesAdd two default  Show help  +▊▁▁▁▁▁▁▁▁▎testing profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add pipeline testingAdd pipeline testing  Show help  +▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Hide help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 844f1dc030..cf92557418 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,256 +19,256 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3616702486-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3616702486-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #94999c } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: 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} +.terminal-3616702486-r9 { fill: #507bb3 } +.terminal-3616702486-r10 { fill: #808080 } +.terminal-3616702486-r11 { fill: #dde6ed;font-weight: bold } +.terminal-3616702486-r12 { fill: #001541 } +.terminal-3616702486-r13 { fill: #14191f } +.terminal-3616702486-r14 { fill: #454a50 } +.terminal-3616702486-r15 { fill: #7ae998 } +.terminal-3616702486-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3616702486-r17 { fill: #0a180e;font-weight: bold } +.terminal-3616702486-r18 { fill: #000000 } +.terminal-3616702486-r19 { fill: #008139 } +.terminal-3616702486-r20 { fill: #fea62b;font-weight: bold } +.terminal-3616702486-r21 { fill: #a7a9ab } +.terminal-3616702486-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous  -Integration (CI) testing▃▃ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common  -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add configuration filesThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing  -custom parameters  -required to run nf-core  -pipelines at different  -institutions - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use code lintersThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include code linters and▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -CI tests to lint your  -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎        Toggle all features +▊▁▁▁▁▁▁▁▁▎ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges▇▇ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a changelogAdd a CHANGELOG.md  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add testing profilesAdd two default  Show help  +▊▁▁▁▁▁▁▁▁▎testing profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add pipeline testingAdd pipeline testing  Show help  +▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 2d2adfce98..c18bb31b8e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,253 +19,254 @@ font-weight: 700; } - .terminal-721554407-matrix { + .terminal-1108014852-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-721554407-title { + .terminal-1108014852-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-721554407-r1 { fill: #c5c8c6 } -.terminal-721554407-r2 { fill: #e0e0e0 } -.terminal-721554407-r3 { fill: #94999c } -.terminal-721554407-r4 { fill: #0178d4;font-weight: bold } -.terminal-721554407-r5 { fill: #121212 } -.terminal-721554407-r6 { fill: #191919 } -.terminal-721554407-r7 { fill: #6db2ff } -.terminal-721554407-r8 { fill: 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#dde6ed;font-weight: bold } +.terminal-1108014852-r11 { fill: #001541 } +.terminal-1108014852-r12 { fill: #454a50 } +.terminal-1108014852-r13 { fill: #7ae998 } +.terminal-1108014852-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-1108014852-r15 { fill: #0a180e;font-weight: bold } +.terminal-1108014852-r16 { fill: #000000 } +.terminal-1108014852-r17 { fill: #008139 } +.terminal-1108014852-r18 { fill: #fea62b;font-weight: bold } +.terminal-1108014852-r19 { fill: #a7a9ab } +.terminal-1108014852-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common  -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report  -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control  -analysis of input FASTQ  -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema  Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - - - - - - - - - - - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use multiqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use fastqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + + + + + + + + + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg 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-▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  From 393dcf20a33ebbe5bf38a47ad38b529699a19daa Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Tue, 17 Jun 2025 10:21:47 +0200 Subject: [PATCH 06/33] test snaps --- .../downstream_samplesheet.nf.test.snap | 116 ++++++ .github/snapshots/gpu.nf.test.snap | 116 ++++++ log.txt | 351 ++++++++++++++++++ 3 files changed, 583 insertions(+) create mode 100644 .github/snapshots/downstream_samplesheet.nf.test.snap create mode 100644 .github/snapshots/gpu.nf.test.snap diff --git a/.github/snapshots/downstream_samplesheet.nf.test.snap b/.github/snapshots/downstream_samplesheet.nf.test.snap new file mode 100644 index 0000000000..b21a89180d --- /dev/null +++ b/.github/snapshots/downstream_samplesheet.nf.test.snap @@ -0,0 +1,116 @@ +{ + "-profile test": { + "content": [ + 4, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, + [ + "fastqc", + "fastqc/SAMPLE1_PE_1_fastqc.html", + "fastqc/SAMPLE1_PE_1_fastqc.zip", + "fastqc/SAMPLE1_PE_2_fastqc.html", + "fastqc/SAMPLE1_PE_2_fastqc.zip", + "fastqc/SAMPLE2_PE_1_fastqc.html", + "fastqc/SAMPLE2_PE_1_fastqc.zip", + "fastqc/SAMPLE2_PE_2_fastqc.html", + "fastqc/SAMPLE2_PE_2_fastqc.zip", + "fastqc/SAMPLE3_SE_1_fastqc.html", + "fastqc/SAMPLE3_SE_1_fastqc.zip", + "fastqc/SAMPLE3_SE_2_fastqc.html", + "fastqc/SAMPLE3_SE_2_fastqc.zip", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + 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"multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", + "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", + "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/png", + 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"multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", + "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_testpipeline_software_mqc_versions.yml" + ], + [ + "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", + "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", + "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", + "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", + "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", + "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", + "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", + "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", + "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78" + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.5" + }, + "timestamp": "2025-06-16T14:29:10.076573" + } +} \ No newline at end of file diff --git a/log.txt b/log.txt index e69de29bb2..9fa5222e33 100644 --- a/log.txt +++ b/log.txt @@ -0,0 +1,351 @@ +[2025-06-16 14:25:08,123] nf_core.pipelines.create.create [DEBUG ] Could not read init.defaultBranch +[2025-06-16 14:25:08,123] nf_core.utils [DEBUG ] Could not find a config file in the directory '.' +[2025-06-16 14:25:08,151] nf_core.pipelines.create.create [INFO ] Creating new pipeline: 'testpipeline' +[2025-06-16 14:25:08,184] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CODE_OF_CONDUCT.md' +[2025-06-16 14:25:08,187] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CODE_OF_CONDUCT.md' +[2025-06-16 14:25:08,187] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'LICENSE' +[2025-06-16 14:25:08,188] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/LICENSE' +[2025-06-16 14:25:08,189] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CHANGELOG.md' +[2025-06-16 14:25:08,190] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CHANGELOG.md' +[2025-06-16 14:25:08,190] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tower.yml' +[2025-06-16 14:25:08,192] nf_core.pipelines.create.create [DEBUG ] 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'/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow.config' +[2025-06-16 14:25:08,221] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitignore' +[2025-06-16 14:25:08,222] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitignore' +[2025-06-16 14:25:08,222] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CITATIONS.md' +[2025-06-16 14:25:08,224] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CITATIONS.md' +[2025-06-16 14:25:08,225] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitattributes' +[2025-06-16 14:25:08,225] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitattributes' +[2025-06-16 14:25:08,226] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow_schema.json' 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'subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config' +[2025-06-16 14:25:08,454] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/nextflow.config' +[2025-06-16 14:25:08,454] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test' +[2025-06-16 14:25:08,456] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/subworkflows/nf-core/utils_nfcore_pipeline/tests/main.workflow.nf.test' +[2025-06-16 14:25:08,456] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'subworkflows/local/utils_nfcore_pipeline_pipeline/main.nf' +[2025-06-16 14:25:08,465] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/subworkflows/local/utils_nfcore_testpipeline_pipeline/main.nf' +[2025-06-16 14:25:08,465] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CODE_OF_CONDUCT.md' +[2025-06-16 14:25:08,466] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CODE_OF_CONDUCT.md' +[2025-06-16 14:25:08,466] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'LICENSE' +[2025-06-16 14:25:08,466] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/LICENSE' +[2025-06-16 14:25:08,467] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CHANGELOG.md' +[2025-06-16 14:25:08,467] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CHANGELOG.md' +[2025-06-16 14:25:08,467] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tower.yml' +[2025-06-16 14:25:08,468] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/tower.yml' +[2025-06-16 14:25:08,468] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.pre-commit-config.yaml' +[2025-06-16 14:25:08,468] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.pre-commit-config.yaml' +[2025-06-16 14:25:08,469] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.nf-core.yml' +[2025-06-16 14:25:08,469] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml' +[2025-06-16 14:25:08,469] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.prettierignore' +[2025-06-16 14:25:08,470] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.prettierignore' +[2025-06-16 14:25:08,470] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'README.md' +[2025-06-16 14:25:08,470] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/README.md' +[2025-06-16 14:25:08,471] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nf-test.config' +[2025-06-16 14:25:08,471] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nf-test.config' +[2025-06-16 14:25:08,472] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.prettierrc.yml' +[2025-06-16 14:25:08,472] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.prettierrc.yml' +[2025-06-16 14:25:08,472] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow.config' +[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow.config' +[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitignore' +[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitignore' +[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CITATIONS.md' +[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CITATIONS.md' +[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitattributes' +[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitattributes' +[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow_schema.json' +[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow_schema.json' +[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitpod.yml' +[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitpod.yml' +[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules.json' +[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules.json' +[2025-06-16 14:25:08,477] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'main.nf' +[2025-06-16 14:25:08,477] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/main.nf' +[2025-06-16 14:25:08,478] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_light_2300.png. Reusing this file. +[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 +[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 +[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' +[2025-06-16 14:25:08,510] PIL.PngImagePlugin [DEBUG ] Compression method 0 +[2025-06-16 14:25:08,510] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 65536 +[2025-06-16 14:25:08,661] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/nf-core-testpipeline_logo_light.png' +[2025-06-16 14:25:08,662] nf_core.pipelines.create_logo [DEBUG ] Creating directory /Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images +[2025-06-16 14:25:08,662] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_dark_600.png. Reusing this file. +[2025-06-16 14:25:08,662] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 +[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 +[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' +[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] Compression method 0 +[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 28861 +[2025-06-16 14:25:08,674] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images/nf-core-testpipeline_logo_dark.png' +[2025-06-16 14:25:08,675] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_light_600.png. Reusing this file. +[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 +[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 +[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' +[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] Compression method 0 +[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 24287 +[2025-06-16 14:25:08,686] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images/nf-core-testpipeline_logo_light.png' +[2025-06-16 14:25:08,701] nf_core.utils [DEBUG ] Could not find git hash for pipeline: /Users/yuxinning/Projects/tools/nf-core-testpipeline. /Users/yuxinning/Projects/tools/nf-core-testpipeline +[2025-06-16 14:25:08,701] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path +[2025-06-16 14:25:08,702] nf_core.utils [DEBUG ] No config cache found +[2025-06-16 14:25:08,702] nf_core.utils [DEBUG ] Running command: nextflow config -flat /Users/yuxinning/Projects/tools/nf-core-testpipeline +[2025-06-16 14:25:12,625] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ------------------------------------------------------ +[2025-06-16 14:25:12,625] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ,--./,-. +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  ___ __ __ __ ___ /,-._.--~' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  |\ | |__ __ / ` / \ |__) |__ } { +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  | \| | \__, \__/ | \ |___ \`-._,-`-, +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + `._,._,' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  nf-core/testpipeline 1.0.0dev +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ------------------------------------------------------ +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + * The nf-core framework +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + https://doi.org/10.1038/s41587-020-0439-x +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + * Software dependencies +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + https://github.com/nf-core/testpipeline/blob/master/CITATIONS.md +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ------------------------------------------------------ +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ,--./,-. +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  ___ __ __ __ ___ /,-._.--~' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  |\ | |__ __ / ` / \ |__) |__ } { +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  | \| | \__, \__/ | \ |___ \`-._,-`-, +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + `._,._,' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: +  nf-core/testpipeline 1.0.0dev +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ------------------------------------------------------ +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ' +[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + * The nf-core framework +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + https://doi.org/10.1038/s41587-020-0439-x +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + * Software dependencies +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + https://github.com/nf-core/testpipeline/blob/master/CITATIONS.md +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: + ' +[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Saving config cache: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json +[2025-06-16 14:25:12,629] nf_core.utils [DEBUG ] No conda `environment.yml` file found. +[2025-06-16 14:25:12,639] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): nf-co.re:443 +[2025-06-16 14:25:12,941] urllib3.connectionpool [DEBUG ] https://nf-co.re:443 "GET /pipelines.json HTTP/1.1" 200 None +[2025-06-16 14:25:13,366] nf_core.pipelines.rocrate [DEBUG ] Adding topics: ['nf-core', 'nextflow'] +[2025-06-16 14:25:13,366] nf_core.pipelines.rocrate [DEBUG ] No git repository found. No git contributors will be added as authors. +[2025-06-16 14:25:13,368] nf_core.pipelines.rocrate [INFO ] Saving metadata file to '/Users/yuxinning/Projects/tools/nf-core-testpipeline' +[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path +[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Found a config cache, loading: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json +[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Using config file: /Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml +[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path +[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Found a config cache, loading: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json +[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Using config file: /Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml +[2025-06-16 14:25:13,376] nf_core.pipelines.create.create [DEBUG ] Dumping pipeline template yml to pipeline config file '.nf-core.yml' +[2025-06-16 14:25:13,376] nf_core.pipelines.create.create [DEBUG ] Running prettier on pipeline files +[2025-06-16 14:25:16,825] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed + +[2025-06-16 14:25:16,826] nf_core.pipelines.create.create [INFO ] Initialising local pipeline git repository +[2025-06-16 14:25:16,830] git.cmd [DEBUG ] Popen(['git', 'init'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) +[2025-06-16 14:25:16,876] git.cmd [DEBUG ] Popen(['git', 'add', '-A'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,163] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,188] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,218] git.cmd [DEBUG ] Popen(['git', 'branch', '-m', 'main', 'master'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,244] git.cmd [DEBUG ] Popen(['git', 'branch', 'TEMPLATE'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,267] git.cmd [DEBUG ] Popen(['git', 'branch', 'dev'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) +[2025-06-16 14:25:17,291] nf_core.pipelines.create.create [INFO ] Done. Remember to add a remote and push to GitHub: +[white on grey23] cd /Users/yuxinning/Projects/tools/nf-core-testpipeline + git remote add origin git@github.com:USERNAME/REPO_NAME.git + git push --all origin +[2025-06-16 14:25:17,296] nf_core.pipelines.create.create [INFO ] This will also push your newly created dev branch and the TEMPLATE branch for syncing. +[2025-06-16 14:25:18,935] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed + +[2025-06-16 14:25:18,935] nf_core.pipelines.create.create [INFO ] [green bold]!!!!!! IMPORTANT !!!!!! + +[green not bold]If you are interested in adding your pipeline to the nf-core community, +PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! + +[default]Please read: [link=https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community]https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community[/link] From 39546b6b53e02a01f456ba8bd95e96e3ad9429da Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 10:55:57 +0200 Subject: [PATCH 07/33] remove downstream_samplesheet feature --- .../downstream_samplesheet.nf.test.snap | 116 ------------------ .../pipelines/create/template_features.yml | 12 -- 2 files changed, 128 deletions(-) delete mode 100644 .github/snapshots/downstream_samplesheet.nf.test.snap diff --git a/.github/snapshots/downstream_samplesheet.nf.test.snap b/.github/snapshots/downstream_samplesheet.nf.test.snap deleted file mode 100644 index b21a89180d..0000000000 --- a/.github/snapshots/downstream_samplesheet.nf.test.snap +++ /dev/null @@ -1,116 +0,0 @@ -{ - "-profile test": { - "content": [ - 4, - { - "FASTQC": { - "fastqc": "0.12.1" - }, - "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" - } - }, - [ - "fastqc", - "fastqc/SAMPLE1_PE_1_fastqc.html", - "fastqc/SAMPLE1_PE_1_fastqc.zip", - "fastqc/SAMPLE1_PE_2_fastqc.html", - "fastqc/SAMPLE1_PE_2_fastqc.zip", - "fastqc/SAMPLE2_PE_1_fastqc.html", - "fastqc/SAMPLE2_PE_1_fastqc.zip", - "fastqc/SAMPLE2_PE_2_fastqc.html", - "fastqc/SAMPLE2_PE_2_fastqc.zip", - "fastqc/SAMPLE3_SE_1_fastqc.html", - "fastqc/SAMPLE3_SE_1_fastqc.zip", - "fastqc/SAMPLE3_SE_2_fastqc.html", - "fastqc/SAMPLE3_SE_2_fastqc.zip", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", - "multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", - "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", - "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", - "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc_citations.txt", - "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_fastqc.txt", - "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_software_versions.txt", - "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", - "multiqc/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/fastqc-status-check-heatmap.png", - "multiqc/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png", - "multiqc/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png", - "multiqc/multiqc_plots/png/general_stats_table.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg", - "multiqc/multiqc_plots/svg/general_stats_table.svg", - "multiqc/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_testpipeline_software_mqc_versions.yml" - ], - [ - "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", - "fastqc_overrepresented_sequences_plot.txt:md5,4b23cea39c4e23deef6b97810bc1ee46", - "fastqc_per_base_n_content_plot.txt:md5,037692101c0130c72493d3bbfa3afac1", - "fastqc_per_base_sequence_quality_plot.txt:md5,bfe735f3e31befe13bdf6761bb297d6e", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,7108d19c46ef7883e864ba274c457d2e", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,23f527c80a148e4f34e5a43f6e520a90", - "fastqc_per_sequence_quality_scores_plot.txt:md5,a0cc0e6df7bfb05257da1cfc88b13c50", - "fastqc_sequence_counts_plot.txt:md5,c6e4e1588e6765fe8df27812a1322fbd", - "fastqc_sequence_duplication_levels_plot.txt:md5,3cde2db4033f6c64648976d1174db925", - "fastqc_sequence_length_distribution_plot.txt:md5,e82b9b14a7e24c0c5f27af97cebb6870", - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "multiqc_fastqc.txt:md5,1a41c2158adc9947bff9232962f70110", - "multiqc_general_stats.txt:md5,0b54e4e764665bd57fe0f95216744a78" - ] - ], - "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.5" - }, - "timestamp": "2025-06-16T14:29:10.076573" - } -} \ No newline at end of file diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index dbb694cb00..9485020bdd 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -294,18 +294,6 @@ nf_schema: custom_pipelines: True default: true -downstream_samplesheet: - skippable_paths: - - "subworkflows" - short_description: "Generate downstream samplesheets" - description: "The pipeline will include the generate_downstream_samplesheets subworkflow for the generation of a samplesheet for other downstream pipelines." - help_text: | - The pipeline will include the generate_downstream_samplesheets subworkflow. - The subworkflow generate_downstream_samplesheets provides a base template for generating samplesheets by taking a specified input channel of i.e. reads or fasta extracts its metadata for generating samplesheets. - nfcore_pipelines: False - custom_pipelines: True - default: true - gpu: skippable_paths: False short_description: "Use GPU" From 5039d8c119e1ef9b6e38b2b310e58c974db4d2d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 10:56:23 +0200 Subject: [PATCH 08/33] remove unwanted log.txt --- log.txt | 351 -------------------------------------------------------- 1 file changed, 351 deletions(-) delete mode 100644 log.txt diff --git a/log.txt b/log.txt deleted file mode 100644 index 9fa5222e33..0000000000 --- a/log.txt +++ /dev/null @@ -1,351 +0,0 @@ -[2025-06-16 14:25:08,123] nf_core.pipelines.create.create [DEBUG ] Could not read init.defaultBranch -[2025-06-16 14:25:08,123] nf_core.utils [DEBUG ] Could not find a config file in the directory '.' -[2025-06-16 14:25:08,151] nf_core.pipelines.create.create [INFO ] Creating new pipeline: 'testpipeline' -[2025-06-16 14:25:08,184] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CODE_OF_CONDUCT.md' -[2025-06-16 14:25:08,187] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CODE_OF_CONDUCT.md' -[2025-06-16 14:25:08,187] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'LICENSE' -[2025-06-16 14:25:08,188] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/LICENSE' -[2025-06-16 14:25:08,189] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CHANGELOG.md' -[2025-06-16 14:25:08,190] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CHANGELOG.md' -[2025-06-16 14:25:08,190] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tower.yml' -[2025-06-16 14:25:08,192] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/tower.yml' -[2025-06-16 14:25:08,192] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.pre-commit-config.yaml' -[2025-06-16 14:25:08,194] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.pre-commit-config.yaml' -[2025-06-16 14:25:08,195] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.nf-core.yml' -[2025-06-16 14:25:08,197] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml' -[2025-06-16 14:25:08,198] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.prettierignore' -[2025-06-16 14:25:08,200] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.prettierignore' -[2025-06-16 14:25:08,200] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'README.md' -[2025-06-16 14:25:08,207] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/README.md' -[2025-06-16 14:25:08,208] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nf-test.config' -[2025-06-16 14:25:08,209] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nf-test.config' -[2025-06-16 14:25:08,209] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.prettierrc.yml' -[2025-06-16 14:25:08,211] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.prettierrc.yml' -[2025-06-16 14:25:08,212] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow.config' -[2025-06-16 14:25:08,220] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow.config' -[2025-06-16 14:25:08,221] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitignore' -[2025-06-16 14:25:08,222] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitignore' -[2025-06-16 14:25:08,222] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CITATIONS.md' -[2025-06-16 14:25:08,224] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CITATIONS.md' -[2025-06-16 14:25:08,225] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitattributes' -[2025-06-16 14:25:08,225] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitattributes' -[2025-06-16 14:25:08,226] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow_schema.json' -[2025-06-16 14:25:08,231] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow_schema.json' -[2025-06-16 14:25:08,231] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitpod.yml' -[2025-06-16 14:25:08,232] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitpod.yml' -[2025-06-16 14:25:08,232] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules.json' -[2025-06-16 14:25:08,235] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules.json' -[2025-06-16 14:25:08,235] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'main.nf' -[2025-06-16 14:25:08,241] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/main.nf' -[2025-06-16 14:25:08,241] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tests/.nftignore' -[2025-06-16 14:25:08,243] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/tests/.nftignore' -[2025-06-16 14:25:08,243] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tests/default.nf.test' -[2025-06-16 14:25:08,245] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/tests/default.nf.test' -[2025-06-16 14:25:08,245] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'tests/nextflow.config' -[2025-06-16 14:25:08,247] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/tests/nextflow.config' -[2025-06-16 14:25:08,247] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'workflows/pipeline.nf' -[2025-06-16 14:25:08,252] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/workflows/testpipeline.nf' -[2025-06-16 14:25:08,252] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'docs/usage.md' -[2025-06-16 14:25:08,257] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/usage.md' -[2025-06-16 14:25:08,257] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'docs/output.md' -[2025-06-16 14:25:08,260] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/output.md' -[2025-06-16 14:25:08,261] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'docs/README.md' -[2025-06-16 14:25:08,263] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/README.md' -[2025-06-16 14:25:08,263] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.devcontainer/devcontainer.json' -[2025-06-16 14:25:08,264] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.devcontainer/devcontainer.json' -[2025-06-16 14:25:08,264] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.github/PULL_REQUEST_TEMPLATE.md' -[2025-06-16 14:25:08,267] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.github/PULL_REQUEST_TEMPLATE.md' -[2025-06-16 14:25:08,267] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.github/.dockstore.yml' -[2025-06-16 14:25:08,269] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.github/.dockstore.yml' -[2025-06-16 14:25:08,269] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.github/CONTRIBUTING.md' -[2025-06-16 14:25:08,277] 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'/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/schema_input.json' -[2025-06-16 14:25:08,292] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/multiqc_config.yml' -[2025-06-16 14:25:08,297] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/multiqc_config.yml' -[2025-06-16 14:25:08,297] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/email_template.txt' -[2025-06-16 14:25:08,301] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/email_template.txt' -[2025-06-16 14:25:08,301] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/slackreport.json' -[2025-06-16 14:25:08,303] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/slackreport.json' -[2025-06-16 14:25:08,304] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/sendmail_template.txt' -[2025-06-16 14:25:08,307] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/sendmail_template.txt' -[2025-06-16 14:25:08,307] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/samplesheet.csv' -[2025-06-16 14:25:08,308] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/samplesheet.csv' -[2025-06-16 14:25:08,309] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/adaptivecard.json' -[2025-06-16 14:25:08,311] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/adaptivecard.json' -[2025-06-16 14:25:08,312] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'assets/methods_description_template.yml' -[2025-06-16 14:25:08,315] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/methods_description_template.yml' -[2025-06-16 14:25:08,315] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/test_full.config' -[2025-06-16 14:25:08,318] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/test_full.config' -[2025-06-16 14:25:08,319] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/base.config' -[2025-06-16 14:25:08,321] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/base.config' -[2025-06-16 14:25:08,321] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/test.config' -[2025-06-16 14:25:08,323] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/test.config' -[2025-06-16 14:25:08,324] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/igenomes.config' -[2025-06-16 14:25:08,332] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/igenomes.config' -[2025-06-16 14:25:08,332] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/modules.config' -[2025-06-16 14:25:08,335] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/modules.config' -[2025-06-16 14:25:08,335] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'conf/igenomes_ignored.config' -[2025-06-16 14:25:08,337] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/conf/igenomes_ignored.config' -[2025-06-16 14:25:08,338] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules/nf-core/multiqc/environment.yml' -[2025-06-16 14:25:08,339] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules/nf-core/multiqc/environment.yml' -[2025-06-16 14:25:08,339] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules/nf-core/multiqc/meta.yml' -[2025-06-16 14:25:08,341] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules/nf-core/multiqc/meta.yml' -[2025-06-16 14:25:08,341] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules/nf-core/multiqc/main.nf' -[2025-06-16 14:25:08,343] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules/nf-core/multiqc/main.nf' -[2025-06-16 14:25:08,344] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 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-[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow.config' -[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitignore' -[2025-06-16 14:25:08,473] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitignore' -[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'CITATIONS.md' -[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/CITATIONS.md' -[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitattributes' -[2025-06-16 14:25:08,474] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitattributes' -[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'nextflow_schema.json' -[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/nextflow_schema.json' -[2025-06-16 14:25:08,475] nf_core.pipelines.create.create [DEBUG ] Rendering template file: '.gitpod.yml' -[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/.gitpod.yml' -[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'modules.json' -[2025-06-16 14:25:08,476] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/modules.json' -[2025-06-16 14:25:08,477] nf_core.pipelines.create.create [DEBUG ] Rendering template file: 'main.nf' -[2025-06-16 14:25:08,477] nf_core.pipelines.create.create [DEBUG ] Writing to output file: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/main.nf' -[2025-06-16 14:25:08,478] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_light_2300.png. Reusing this file. -[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 -[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 -[2025-06-16 14:25:08,509] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' -[2025-06-16 14:25:08,510] PIL.PngImagePlugin [DEBUG ] Compression method 0 -[2025-06-16 14:25:08,510] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 65536 -[2025-06-16 14:25:08,661] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/assets/nf-core-testpipeline_logo_light.png' -[2025-06-16 14:25:08,662] nf_core.pipelines.create_logo [DEBUG ] Creating directory /Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images -[2025-06-16 14:25:08,662] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_dark_600.png. Reusing this file. -[2025-06-16 14:25:08,662] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 -[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 -[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' -[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] Compression method 0 -[2025-06-16 14:25:08,663] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 28861 -[2025-06-16 14:25:08,674] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images/nf-core-testpipeline_logo_dark.png' -[2025-06-16 14:25:08,675] nf_core.pipelines.create_logo [DEBUG ] Logo already exists in cache at: /Users/yuxinning/.cache/nfcore/logo/nf-core-testpipeline_logo_light_600.png. Reusing this file. -[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'IHDR' 16 13 -[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'iCCP' 41 379 -[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] iCCP profile name b'ICC Profile' -[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] Compression method 0 -[2025-06-16 14:25:08,676] PIL.PngImagePlugin [DEBUG ] STREAM b'IDAT' 432 24287 -[2025-06-16 14:25:08,686] nf_core.pipelines.create_logo [DEBUG ] Saved logo to: '/Users/yuxinning/Projects/tools/nf-core-testpipeline/docs/images/nf-core-testpipeline_logo_light.png' -[2025-06-16 14:25:08,701] nf_core.utils [DEBUG ] Could not find git hash for pipeline: /Users/yuxinning/Projects/tools/nf-core-testpipeline. /Users/yuxinning/Projects/tools/nf-core-testpipeline -[2025-06-16 14:25:08,701] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path -[2025-06-16 14:25:08,702] nf_core.utils [DEBUG ] No config cache found -[2025-06-16 14:25:08,702] nf_core.utils [DEBUG ] Running command: nextflow config -flat /Users/yuxinning/Projects/tools/nf-core-testpipeline -[2025-06-16 14:25:12,625] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ------------------------------------------------------ -[2025-06-16 14:25:12,625] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ,--./,-. -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  ___ __ __ __ ___ /,-._.--~' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  |\ | |__ __ / ` / \ |__) |__ } { -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  | \| | \__, \__/ | \ |___ \`-._,-`-, -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - `._,._,' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  nf-core/testpipeline 1.0.0dev -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ------------------------------------------------------ -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - * The nf-core framework -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - https://doi.org/10.1038/s41587-020-0439-x -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - * Software dependencies -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - https://github.com/nf-core/testpipeline/blob/master/CITATIONS.md -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ------------------------------------------------------ -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ,--./,-. -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  ___ __ __ __ ___ /,-._.--~' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  |\ | |__ __ / ` / \ |__) |__ } { -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  | \| | \__, \__/ | \ |___ \`-._,-`-, -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - `._,._,' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: -  nf-core/testpipeline 1.0.0dev -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ------------------------------------------------------ -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ' -[2025-06-16 14:25:12,626] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - * The nf-core framework -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - https://doi.org/10.1038/s41587-020-0439-x -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - * Software dependencies -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - https://github.com/nf-core/testpipeline/blob/master/CITATIONS.md -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Couldn't find key=value config pair: - ' -[2025-06-16 14:25:12,627] nf_core.utils [DEBUG ] Saving config cache: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json -[2025-06-16 14:25:12,629] nf_core.utils [DEBUG ] No conda `environment.yml` file found. -[2025-06-16 14:25:12,639] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): nf-co.re:443 -[2025-06-16 14:25:12,941] urllib3.connectionpool [DEBUG ] https://nf-co.re:443 "GET /pipelines.json HTTP/1.1" 200 None -[2025-06-16 14:25:13,366] nf_core.pipelines.rocrate [DEBUG ] Adding topics: ['nf-core', 'nextflow'] -[2025-06-16 14:25:13,366] nf_core.pipelines.rocrate [DEBUG ] No git repository found. No git contributors will be added as authors. -[2025-06-16 14:25:13,368] nf_core.pipelines.rocrate [INFO ] Saving metadata file to '/Users/yuxinning/Projects/tools/nf-core-testpipeline' -[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path -[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Found a config cache, loading: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json -[2025-06-16 14:25:13,371] nf_core.utils [DEBUG ] Using config file: /Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml -[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Got '/Users/yuxinning/Projects/tools/nf-core-testpipeline' as path -[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Found a config cache, loading: /Users/yuxinning/.nextflow/nf-core/wf-config-cache-d72560874485c11774c06d2aa.json -[2025-06-16 14:25:13,374] nf_core.utils [DEBUG ] Using config file: /Users/yuxinning/Projects/tools/nf-core-testpipeline/.nf-core.yml -[2025-06-16 14:25:13,376] nf_core.pipelines.create.create [DEBUG ] Dumping pipeline template yml to pipeline config file '.nf-core.yml' -[2025-06-16 14:25:13,376] nf_core.pipelines.create.create [DEBUG ] Running prettier on pipeline files -[2025-06-16 14:25:16,825] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed - -[2025-06-16 14:25:16,826] nf_core.pipelines.create.create [INFO ] Initialising local pipeline git repository -[2025-06-16 14:25:16,830] git.cmd [DEBUG ] Popen(['git', 'init'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) -[2025-06-16 14:25:16,876] git.cmd [DEBUG ] Popen(['git', 'add', '-A'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,163] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch-check'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,188] git.cmd [DEBUG ] Popen(['git', 'cat-file', '--batch'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,218] git.cmd [DEBUG ] Popen(['git', 'branch', '-m', 'main', 'master'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,244] git.cmd [DEBUG ] Popen(['git', 'branch', 'TEMPLATE'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,267] git.cmd [DEBUG ] Popen(['git', 'branch', 'dev'], cwd=/Users/yuxinning/Projects/tools/nf-core-testpipeline, stdin=None, shell=False, universal_newlines=False) -[2025-06-16 14:25:17,291] nf_core.pipelines.create.create [INFO ] Done. Remember to add a remote and push to GitHub: -[white on grey23] cd /Users/yuxinning/Projects/tools/nf-core-testpipeline - git remote add origin git@github.com:USERNAME/REPO_NAME.git - git push --all origin -[2025-06-16 14:25:17,296] nf_core.pipelines.create.create [INFO ] This will also push your newly created dev branch and the TEMPLATE branch for syncing. -[2025-06-16 14:25:18,935] nf_core.pipelines.lint_utils [DEBUG ] prettier.................................................................Passed - -[2025-06-16 14:25:18,935] nf_core.pipelines.create.create [INFO ] [green bold]!!!!!! IMPORTANT !!!!!! - -[green not bold]If you are interested in adding your pipeline to the nf-core community, -PLEASE COME AND TALK TO US IN THE NF-CORE SLACK BEFORE WRITING ANY CODE! - -[default]Please read: [link=https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community]https://nf-co.re/docs/tutorials/adding_a_pipeline/overview#join-the-community[/link] From d08e3f254d2e3c0cf1aab2d2e22ac526a1ddb6de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 11:35:20 +0200 Subject: [PATCH 09/33] use feature sections to classify the switches --- nf_core/pipelines/create/custompipeline.py | 31 +- nf_core/pipelines/create/nfcorepipeline.py | 30 +- .../pipelines/create/template_features.yml | 1150 +++++++++-------- 3 files changed, 622 insertions(+), 589 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 83cc303ca0..0d45feedb7 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -36,18 +36,27 @@ def compose(self) -> ComposeResult: ) def on_mount(self) -> None: - for name, feature in self.parent.template_features_yml.items(): - if feature["custom_pipelines"]: - self.query_one("#features").mount( - PipelineFeature( - feature["help_text"], - feature["short_description"], - feature["description"], - name, - feature["default"], + for section_name, section in self.parent.template_features_yml.items(): + section_title = section["name"] + features = section["features"] + show_section = False + self.query_one("#features").mount( + Markdown(section_title, id=section_name), + ) + for name, feature in features.items(): + if feature["custom_pipelines"]: + show_section = True + self.query_one("#features").mount( + PipelineFeature( + feature["help_text"], + feature["short_description"], + feature["description"], + name, + feature["default"], + ) ) - ) - self.query_one("#toggle_all", Switch).value = False + if not show_section: + self.query_one("#features").query_one(f"#{section_name}").remove() @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: diff --git a/nf_core/pipelines/create/nfcorepipeline.py b/nf_core/pipelines/create/nfcorepipeline.py index 9260bbbc8f..d86f236387 100644 --- a/nf_core/pipelines/create/nfcorepipeline.py +++ b/nf_core/pipelines/create/nfcorepipeline.py @@ -30,17 +30,27 @@ def compose(self) -> ComposeResult: ) def on_mount(self) -> None: - for name, feature in self.parent.template_features_yml.items(): - if feature["nfcore_pipelines"]: - self.query_one("#features").mount( - PipelineFeature( - feature["help_text"], - feature["short_description"], - feature["description"], - name, - feature["default"], + for section_name, section in self.parent.template_features_yml.items(): + section_title = section["name"] + features = section["features"] + show_section = False + self.query_one("#features").mount( + Markdown(section_title, id=section_name), + ) + for name, feature in features.items(): + if feature["nfcore_pipelines"]: + show_section = True + self.query_one("#features").mount( + PipelineFeature( + feature["help_text"], + feature["short_description"], + feature["description"], + name, + feature["default"], + ) ) - ) + if not show_section: + self.query_one("#features").query_one(f"#{section_name}").remove() @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 9485020bdd..76b6857365 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -1,568 +1,582 @@ -# Repository Setup -github: - skippable_paths: - - ".github" - - ".gitattributes" - short_description: "Use a GitHub repository." - description: "Create a GitHub repository for the pipeline." - help_text: | - This will create a GitHub repository for the pipeline. - - The repository will include: - - Continuous Integration (CI) tests - - Issues and pull requests templates - - The initialisation of a git repository is required to use the nf-core/tools. - This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file. - linting: - files_exist: - - ".github/ISSUE_TEMPLATE/bug_report.yml" - - ".github/ISSUE_TEMPLATE/feature_request.yml" - - ".github/PULL_REQUEST_TEMPLATE.md" - - ".github/CONTRIBUTING.md" - - ".github/.dockstore.yml" - files_unchanged: - - ".github/ISSUE_TEMPLATE/bug_report.yml" - - ".github/ISSUE_TEMPLATE/config.yml" - - ".github/ISSUE_TEMPLATE/feature_request.yml" - - ".github/PULL_REQUEST_TEMPLATE.md" - - ".github/workflows/branch.yml" - - ".github/workflows/linting_comment.yml" - - ".github/workflows/linting.yml" - - ".github/CONTRIBUTING.md" - - ".github/.dockstore.yml" - readme: - - "nextflow_badge" - nfcore_pipelines: False - custom_pipelines: True - default: True - -github_badges: - skippable_paths: False - short_description: "Add Github badges" - description: "The README.md file of the pipeline will include GitHub badges" - help_text: | - The pipeline `README.md` will include badges for: - * AWS CI Tests - * Zenodo DOI - * Nextflow - * nf-core template version - * Conda - * Docker - * Singularity - * Launching on Nextflow Tower - linting: - readme: - - "nextflow_badge" - - "nfcore_template_badge" - nfcore_pipelines: False - custom_pipelines: True - default: True - -changelog: - skippable_paths: - - "CHANGELOG.md" - short_description: "Add a changelog" - description: "Add a CHANGELOG.md file." - help_text: | - Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. - - You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ - linting: - files_exist: - - "CHANGELOG.md" - nfcore_pipelines: False - custom_pipelines: True - default: true - -license: - skippable_paths: - - "LICENSE" - short_description: "Add a license File" - description: "Add the MIT license file." - help_text: | - To protect the copyright of the pipeline, you can add a LICENSE file. - This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT - linting: - files_exist: - - "LICENSE" - files_unchanged: - - "LICENSE" - nfcore_pipelines: False - custom_pipelines: True - default: true - -# Continuous Integration & Testing - -ci: - skippable_paths: - - ".github/workflows/" - short_description: "Add Github CI tests" - description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing" - help_text: | - Nf-core provides a set of Continuous Integration (CI) tests for Github. - When you open a pull request (PR) on your pipeline repository, these tests will run automatically. - - There are different types of tests: - * Linting tests check that your code is formatted correctly and that it adheres to nf-core standards - For code linting they will use [prettier](https://prettier.io/). - * Pipeline tests run your pipeline on a small dataset to check that it works - These tests are run with a small test dataset on GitHub and a larger test dataset on AWS - * Marking old issues as stale - linting: - files_exist: - - ".github/workflows/branch.yml" - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - - ".github/workflows/linting_comment.yml" - - ".github/workflows/linting.yml" - nfcore_pipelines: False - custom_pipelines: True - default: true - -test_config: - skippable_paths: - - "conf/test.config" - - "conf/test_full.config" - - ".github/workflows/awsfulltest.yml" - - ".github/workflows/awstest.yml" - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - short_description: "Add testing profiles" - description: "Add two default testing profiles" - help_text: | - This will add two default testing profiles to run the pipeline with different inputs. - You can customise them and add other test profiles. - - These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run -profile test`. - - The pipeline will include two profiles: `test` and `test_full`. - In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario. - linting: - files_exist: - - "conf/test.config" - - "conf/test_full.config" - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - nextflow_config: False - files_unchanged: - - ".github/CONTRIBUTING.md" - - ".github/PULL_REQUEST_TEMPLATE.md" - nfcore_pipelines: False - custom_pipelines: True - default: true - -nf-test: - skippable_paths: - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - - "nf-test.config" - - "tests/default.nf.test" - - "tests/.nftignore" - - "tests/nextflow.config" - short_description: "Add pipeline testing" - description: "Add pipeline testing using nf-test" - help_text: | - This will add pipeline testing with [nf-test](https://www.nf-test.com/). - - Will add and `nf-test.config` file setting up the appropriate configuration to test your pipeline. - On top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests. - - If you skip this feature, you will still be able to test your pipeline with a `test` profile by running the pipeline. - But you won't have the automated CI testing. - You can add CI by yourself. - linting: - files_exist: - - ".github/workflows/nf-test.yml" - - ".github/actions/get-shards/action.yml" - - ".github/actions/nf-test/action.yml" - - "nf-test.config" - - "tests/default.nf.test" - nfcore_pipelines: False - custom_pipelines: True - default: true - -# Components & Modules -igenomes: - skippable_paths: - - "conf/igenomes.config" - - "conf/igenomes_ignored.config" - short_description: "Use reference genomes" - description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes" - help_text: | - Nf-core pipelines are configured to use a copy of the most common reference genome files. - - By selecting this option, your pipeline will include a configuration file specifying the paths to these files. - - The required code to use these files will also be included in the template. - When the pipeline user provides an appropriate genome key, - the pipeline will automatically download the required reference files. - - For more information about reference genomes in nf-core pipelines, - see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes). - linting: - files_exist: - - "conf/igenomes.config" - - "conf/igenomes_ignored.config" - nfcore_pipelines: True - custom_pipelines: True - default: true - -modules: - skippable_paths: - - "conf/base.config" - - "conf/modules.config" - - "modules.json" - - "modules" - - "subworkflows" - short_description: "Use nf-core components" - description: "Include all required files to use nf-core modules and subworkflows" - help_text: | - It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline. - This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands. - linting: - nfcore_components: False - modules_json: False - base_config: False - modules_config: False - files_exist: - - "conf/base.config" - - "conf/modules.config" - - "modules.json" - nfcore_pipelines: False - custom_pipelines: True - default: true - -multiqc: - skippable_paths: - - "assets/multiqc_config.yml" - - "assets/methods_description_template.yml" - - "modules/nf-core/multiqc/" - short_description: "Use multiqc" - description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." - help_text: | - MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. - - The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. - linting: - files_unchanged: - - ".github/CONTRIBUTING.md" - - "assets/sendmail_template.txt" - files_exist: - - "assets/multiqc_config.yml" - multiqc_config: False - nfcore_pipelines: True - custom_pipelines: True - default: true - -fastqc: - skippable_paths: - - "modules/nf-core/fastqc/" - short_description: "Use fastqc" - description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." - help_text: | - FastQC is a tool which provides quality control checks on raw sequencing data. - The pipeline will include the FastQC module. - nfcore_pipelines: True - custom_pipelines: True - default: true - -nf_schema: - skippable_paths: - - "subworkflows/nf-core/utils_nfschema_plugin" - - "nextflow_schema.json" - - "assets/schema_input.json" - - "assets/samplesheet.csv" - short_description: "Use nf-schema" - description: "Use the nf-schema Nextflow plugin for this pipeline." - help_text: | - [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema. - It also provides helper functionality to create help messages, get a summary - of changed parameters and validate and convert a samplesheet to a channel. - linting: - files_exist: - - "nextflow_schema.json" - schema_params: False - schema_lint: False - schema_description: False - nextflow_config: False - nfcore_pipelines: True - custom_pipelines: True - default: true - -gpu: - skippable_paths: False - short_description: "Use GPU" - description: "Add GPU support to the pipeline" - help_text: | - This will add GPU support to the pipeline. It will add a `use_gpu` parameter to the pipeline. - The pipeline will be able to run on GPU-enabled compute environments. - nfcore_pipelines: False - custom_pipelines: True - default: False - -# Configurations -nf_core_configs: - skippable_paths: False - short_description: "Add configuration files" - description: "The pipeline will include configuration profiles containing custom parameters required to run nf-core pipelines at different institutions" - help_text: | - Nf-core has a repository with a collection of configuration profiles. - - Those config files define a set of parameters which are specific to compute environments at different Institutions. - They can be used within all nf-core pipelines. - If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation. - - For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs) - linting: - files_exist: - - "conf/igenomes.config" - nextflow_config: - - "process.cpus" - - "process.memory" - - "process.time" - - "custom_config" - - "params.custom_config_version" - - "params.custom_config_base" - included_configs: False - nfcore_pipelines: False - custom_pipelines: True - default: true - -is_nfcore: - skippable_paths: - - ".github/ISSUE_TEMPLATE/config" - - "CODE_OF_CONDUCT.md" - - ".github/workflows/awsfulltest.yml" - - ".github/workflows/awstest.yml" - - ".github/workflows/release-announcements.yml" - short_description: "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools." - description: "" - help_text: "" - linting: - files_exist: - - "CODE_OF_CONDUCT.md" - - "assets/nf-core-{{short_name}}_logo_light.png" - - "docs/images/nf-core-{{short_name}}_logo_light.png" - - "docs/images/nf-core-{{short_name}}_logo_dark.png" - - ".github/ISSUE_TEMPLATE/config.yml" - - ".github/workflows/awstest.yml" - - ".github/workflows/awsfulltest.yml" - files_unchanged: - - "CODE_OF_CONDUCT.md" - - "assets/nf-core-{{short_name}}_logo_light.png" - - "docs/images/nf-core-{{short_name}}_logo_light.png" - - "docs/images/nf-core-{{short_name}}_logo_dark.png" - - ".github/ISSUE_TEMPLATE/bug_report.yml" - - ".github/CONTRIBUTING.md" - - ".github/PULL_REQUEST_TEMPLATE.md" - - "assets/email_template.txt" - - "docs/README.md" - nextflow_config: - - "manifest.name" - - "manifest.homePage" - - "validation.help.beforeText" - - "validation.help.afterText" - - "validation.summary.beforeText" - - "validation.summary.afterText" - multiqc_config: - - "report_comment" - nfcore_pipelines: False - custom_pipelines: False - default: true - -seqera_platform: - skippable_paths: - - "tower.yml" - short_description: "Add Seqera Platform output" - description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform" - help_text: | - When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options. - - In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform. - You can extend this file adding any other desired configuration. - nfcore_pipelines: False - custom_pipelines: True - default: true - -# Development Environments -gitpod: - skippable_paths: - - ".gitpod.yml" - short_description: "Include a gitpod environment" - description: "Include the configuration required to use Gitpod." - help_text: | - Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. - - Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. - This is useful to have all the tools ready for pipeline development. - nfcore_pipelines: False - custom_pipelines: True - default: true - -codespaces: - skippable_paths: - - ".devcontainer/devcontainer.json" - short_description: "Include GitHub Codespaces" - description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed." - help_text: | - The pipeline will include a devcontainer configuration. - The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. - - Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal. - linting: - files_unchanged: - - ".github/CONTRIBUTING.md" - nfcore_pipelines: False - custom_pipelines: True - default: true - -vscode: - skippable_paths: - - ".vscode" - short_description: "Render website admonitions in VSCode" - description: "Add a VSCode configuration to render website admonitions" - help_text: | - This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website. - - Adds the `.vscode` directory to the pipelinerepository. - nfcore_pipelines: False - custom_pipelines: True - default: true - -# Code Quality -code_linters: - skippable_paths: - - ".pre-commit-config.yaml" - - ".prettierignore" - - ".prettierrc.yml" - - ".github/workflows/fix-linting.yml" - short_description: "Use code linters" - description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." - help_text: | - Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. - Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. - The available code linters are: - - - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. - - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). - linting: - files_exist: - - ".prettierignore" - - ".prettierrc.yml" - nfcore_pipelines: False - custom_pipelines: True - default: true - -# Documentation & Metadata -citations: - skippable_paths: - - "assets/methods_description_template.yml" - - "CITATIONS.md" - short_description: "Include citations" - description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." - help_text: | - If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. - - Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, - and the logics to add this section to the output MultiQC report (if the report is generated). - linting: - files_exist: - - "CITATIONS.md" - nfcore_pipelines: False - custom_pipelines: True - default: true - -documentation: - skippable_paths: - - "docs" - short_description: "Add documentation" - description: "Add documentation to the pipeline" - help_text: | - This will add documentation markdown files where you can describe your pipeline. - It includes: - - docs/README.md: A README file where you can describe the structure of your documentation. - - docs/output.md: A file where you can explain the output generated by the pipeline - - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters. - - These files come with an exemplary documentation structure written. - linting: - files_exist: - - "docs/output.md" - - "docs/README.md" - - "docs/usage.md" - nfcore_pipelines: False - custom_pipelines: True - default: true - -rocrate: - skippable_paths: - - "ro-crate-metadata.json" - short_description: "Add RO-Crate metadata" - description: "Add a RO-Crate metadata file to describe the pipeline" - help_text: | - RO-Crate is a metadata specification to describe research data and software. - This will add a `ro-crate-metadata.json` file to describe the pipeline. - nfcore_pipelines: False - custom_pipelines: True - linting: - files_warn: - - "ro-crate-metadata.json" - files_unchanged: - - ".prettierignore" - default: true - -# Notifications -email: - skippable_paths: - - "assets/email_template.html" - - "assets/sendmail_template.txt" - - "assets/email_template.txt" - short_description: "Enable email updates" - description: "Enable sending emails on pipeline completion." - help_text: | - Enable the option of sending an email which will include pipeline execution reports on pipeline completion. - linting: - files_exist: - - "assets/email_template.html" - - "assets/sendmail_template.txt" - - "assets/email_template.txt" - files_unchanged: - - ".prettierignore" - nfcore_pipelines: False - custom_pipelines: True - default: true - -adaptivecard: - skippable_paths: - - "assets/adaptivecard.json" - short_description: "Support Microsoft Teams notifications" - description: "Enable pipeline status update messages through Microsoft Teams" - help_text: | - This adds an Adaptive Card. A snippets of user interface. - This Adaptive Card is used as a template for pipeline update messages and it is compatible with Microsoft Teams. - linting: - files_unchanged: - - ".prettierignore" - nfcore_pipelines: False - custom_pipelines: True - default: true - -slackreport: - skippable_paths: - - "assets/slackreport.json" - short_description: "Support Slack notifications" - description: "Enable pipeline status update messages through Slack" - help_text: | - This adds an JSON template used as a template for pipeline update messages in Slack. - linting: - files_unchanged: - - ".prettierignore" - nfcore_pipelines: False - custom_pipelines: True - default: true -# newest version bump +repository_setup: + name: "Repository Setup" + features: + github: + skippable_paths: + - ".github" + - ".gitattributes" + short_description: "Use a GitHub repository." + description: "Create a GitHub repository for the pipeline." + help_text: | + This will create a GitHub repository for the pipeline. + + The repository will include: + - Continuous Integration (CI) tests + - Issues and pull requests templates + + The initialisation of a git repository is required to use the nf-core/tools. + This means that even if you unselect this option, your pipeline will still contain a `.git` directory and `.gitignore` file. + linting: + files_exist: + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".github/ISSUE_TEMPLATE/feature_request.yml" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/CONTRIBUTING.md" + - ".github/.dockstore.yml" + files_unchanged: + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/ISSUE_TEMPLATE/feature_request.yml" + - ".github/PULL_REQUEST_TEMPLATE.md" + - ".github/workflows/branch.yml" + - ".github/workflows/linting_comment.yml" + - ".github/workflows/linting.yml" + - ".github/CONTRIBUTING.md" + - ".github/.dockstore.yml" + readme: + - "nextflow_badge" + nfcore_pipelines: False + custom_pipelines: True + default: True + + github_badges: + skippable_paths: False + short_description: "Add Github badges" + description: "The README.md file of the pipeline will include GitHub badges" + help_text: | + The pipeline `README.md` will include badges for: + * AWS CI Tests + * Zenodo DOI + * Nextflow + * nf-core template version + * Conda + * Docker + * Singularity + * Launching on Nextflow Tower + linting: + readme: + - "nextflow_badge" + - "nfcore_template_badge" + nfcore_pipelines: False + custom_pipelines: True + default: True + + changelog: + skippable_paths: + - "CHANGELOG.md" + short_description: "Add a changelog" + description: "Add a CHANGELOG.md file." + help_text: | + Having a `CHANGELOG.md` file in the pipeline root directory is useful to track the changes added to each version. + + You can read more information on the recommended format here: https://keepachangelog.com/en/1.0.0/ + linting: + files_exist: + - "CHANGELOG.md" + nfcore_pipelines: False + custom_pipelines: True + default: true + + license: + skippable_paths: + - "LICENSE" + short_description: "Add a license File" + description: "Add the MIT license file." + help_text: | + To protect the copyright of the pipeline, you can add a LICENSE file. + This option ads the MIT License. You can read the conditions here: https://opensource.org/license/MIT + linting: + files_exist: + - "LICENSE" + files_unchanged: + - "LICENSE" + nfcore_pipelines: False + custom_pipelines: True + default: true + +continuous_integration_testing: + name: "Continuous Integration & Testing" + features: + ci: + skippable_paths: + - ".github/workflows/" + short_description: "Add Github CI tests" + description: "The pipeline will include several GitHub actions for Continuous Integration (CI) testing" + help_text: | + Nf-core provides a set of Continuous Integration (CI) tests for Github. + When you open a pull request (PR) on your pipeline repository, these tests will run automatically. + + There are different types of tests: + * Linting tests check that your code is formatted correctly and that it adheres to nf-core standards + For code linting they will use [prettier](https://prettier.io/). + * Pipeline tests run your pipeline on a small dataset to check that it works + These tests are run with a small test dataset on GitHub and a larger test dataset on AWS + * Marking old issues as stale + linting: + files_exist: + - ".github/workflows/branch.yml" + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + - ".github/workflows/linting_comment.yml" + - ".github/workflows/linting.yml" + nfcore_pipelines: False + custom_pipelines: True + default: true + + test_config: + skippable_paths: + - "conf/test.config" + - "conf/test_full.config" + - ".github/workflows/awsfulltest.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + short_description: "Add testing profiles" + description: "Add two default testing profiles" + help_text: | + This will add two default testing profiles to run the pipeline with different inputs. + You can customise them and add other test profiles. + + These profiles can be used to run the pipeline with a minimal testing dataset with `nextflow run -profile test`. + + The pipeline will include two profiles: `test` and `test_full`. + In nf-core, we typically use the `test` profile to run the pipeline with a minimal dataset and the `test_full` to run the pipeline with a larger dataset that simulates a real-world scenario. + linting: + files_exist: + - "conf/test.config" + - "conf/test_full.config" + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + nextflow_config: False + files_unchanged: + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + nfcore_pipelines: False + custom_pipelines: True + default: true + + nf-test: + skippable_paths: + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + - "nf-test.config" + - "tests/default.nf.test" + - "tests/.nftignore" + - "tests/nextflow.config" + short_description: "Add pipeline testing" + description: "Add pipeline testing using nf-test" + help_text: | + This will add pipeline testing with [nf-test](https://www.nf-test.com/). + + Will add and `nf-test.config` file setting up the appropriate configuration to test your pipeline. + On top of that, it will also add the Continuous Integration (CI) GitHub actions to run these tests. + + If you skip this feature, you will still be able to test your pipeline with a `test` profile by running the pipeline. + But you won't have the automated CI testing. + You can add CI by yourself. + linting: + files_exist: + - ".github/workflows/nf-test.yml" + - ".github/actions/get-shards/action.yml" + - ".github/actions/nf-test/action.yml" + - "nf-test.config" + - "tests/default.nf.test" + nfcore_pipelines: False + custom_pipelines: True + default: true + +components_modules: + name: "Components & Modules" + features: + igenomes: + skippable_paths: + - "conf/igenomes.config" + - "conf/igenomes_ignored.config" + short_description: "Use reference genomes" + description: "The pipeline will be configured to use a copy of the most common reference genome files from iGenomes" + help_text: | + Nf-core pipelines are configured to use a copy of the most common reference genome files. + + By selecting this option, your pipeline will include a configuration file specifying the paths to these files. + + The required code to use these files will also be included in the template. + When the pipeline user provides an appropriate genome key, + the pipeline will automatically download the required reference files. + + For more information about reference genomes in nf-core pipelines, + see the [nf-core docs](https://nf-co.re/docs/usage/reference_genomes). + linting: + files_exist: + - "conf/igenomes.config" + - "conf/igenomes_ignored.config" + nfcore_pipelines: True + custom_pipelines: True + default: true + + modules: + skippable_paths: + - "conf/base.config" + - "conf/modules.config" + - "modules.json" + - "modules" + - "subworkflows" + short_description: "Use nf-core components" + description: "Include all required files to use nf-core modules and subworkflows" + help_text: | + It is *recommended* to use this feature if you want to use modules and subworkflows in your pipeline. + This will add all required files to use nf-core components or any compatible components from private repos by using `nf-core modules` and `nf-core subworkflows` commands. + linting: + nfcore_components: False + modules_json: False + base_config: False + modules_config: False + files_exist: + - "conf/base.config" + - "conf/modules.config" + - "modules.json" + nfcore_pipelines: False + custom_pipelines: True + default: true + + multiqc: + skippable_paths: + - "assets/multiqc_config.yml" + - "assets/methods_description_template.yml" + - "modules/nf-core/multiqc/" + short_description: "Use multiqc" + description: "The pipeline will include the MultiQC module which generates an HTML report for quality control." + help_text: | + MultiQC is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline quality control results can be visualised in the report and further statistics are available in the report data directory. + + The pipeline will include the MultiQC module and will have special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see http://multiqc.info. + linting: + files_unchanged: + - ".github/CONTRIBUTING.md" + - "assets/sendmail_template.txt" + files_exist: + - "assets/multiqc_config.yml" + multiqc_config: False + nfcore_pipelines: True + custom_pipelines: True + default: true + + fastqc: + skippable_paths: + - "modules/nf-core/fastqc/" + short_description: "Use fastqc" + description: "The pipeline will include the FastQC module which performs quality control analysis of input FASTQ files." + help_text: | + FastQC is a tool which provides quality control checks on raw sequencing data. + The pipeline will include the FastQC module. + nfcore_pipelines: True + custom_pipelines: True + default: true + + nf_schema: + skippable_paths: + - "subworkflows/nf-core/utils_nfschema_plugin" + - "nextflow_schema.json" + - "assets/schema_input.json" + - "assets/samplesheet.csv" + short_description: "Use nf-schema" + description: "Use the nf-schema Nextflow plugin for this pipeline." + help_text: | + [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema. + It also provides helper functionality to create help messages, get a summary + of changed parameters and validate and convert a samplesheet to a channel. + linting: + files_exist: + - "nextflow_schema.json" + schema_params: False + schema_lint: False + schema_description: False + nextflow_config: False + nfcore_pipelines: True + custom_pipelines: True + default: true + +configurations: + name: "Configurations" + features: + nf_core_configs: + skippable_paths: False + short_description: "Add configuration files" + description: "The pipeline will include configuration profiles containing custom parameters required to run nf-core pipelines at different institutions" + help_text: | + Nf-core has a repository with a collection of configuration profiles. + + Those config files define a set of parameters which are specific to compute environments at different Institutions. + They can be used within all nf-core pipelines. + If you are likely to be running nf-core pipelines regularly it is a good idea to use or create a custom config file for your organisation. + + For more information about nf-core configuration profiles, see the [nf-core/configs repository](https://github.com/nf-core/configs) + linting: + files_exist: + - "conf/igenomes.config" + nextflow_config: + - "process.cpus" + - "process.memory" + - "process.time" + - "custom_config" + - "params.custom_config_version" + - "params.custom_config_base" + included_configs: False + nfcore_pipelines: False + custom_pipelines: True + default: true + + is_nfcore: + skippable_paths: + - ".github/ISSUE_TEMPLATE/config" + - "CODE_OF_CONDUCT.md" + - ".github/workflows/awsfulltest.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/release-announcements.yml" + short_description: "A custom pipeline which won't be part of the nf-core organisation but be compatible with nf-core/tools." + description: "" + help_text: "" + linting: + files_exist: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_dark.png" + - ".github/ISSUE_TEMPLATE/config.yml" + - ".github/workflows/awstest.yml" + - ".github/workflows/awsfulltest.yml" + files_unchanged: + - "CODE_OF_CONDUCT.md" + - "assets/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_light.png" + - "docs/images/nf-core-{{short_name}}_logo_dark.png" + - ".github/ISSUE_TEMPLATE/bug_report.yml" + - ".github/CONTRIBUTING.md" + - ".github/PULL_REQUEST_TEMPLATE.md" + - "assets/email_template.txt" + - "docs/README.md" + nextflow_config: + - "manifest.name" + - "manifest.homePage" + - "validation.help.beforeText" + - "validation.help.afterText" + - "validation.summary.beforeText" + - "validation.summary.afterText" + multiqc_config: + - "report_comment" + nfcore_pipelines: False + custom_pipelines: False + default: true + + seqera_platform: + skippable_paths: + - "tower.yml" + short_description: "Add Seqera Platform output" + description: "Add a YAML file to specify which output files to upload when launching a pipeline from the Seqera Platform" + help_text: | + When launching a pipeline with the Seqera Platform, a `tower.yml` file can be used to add configuration options. + + In the pipeline template, this file is used to specify the output files of you pipeline which will be shown on the reports tab of Seqera Platform. + You can extend this file adding any other desired configuration. + nfcore_pipelines: False + custom_pipelines: True + default: true + + gpu: + skippable_paths: False + short_description: "Use GPU" + description: "Add GPU support to the pipeline" + help_text: | + This will add GPU support to the pipeline. It will add a `use_gpu` parameter to the pipeline. + The pipeline will be able to run on GPU-enabled compute environments. + nfcore_pipelines: True + custom_pipelines: True + default: False + +development_environments: + name: "Development Environments" + features: + gitpod: + skippable_paths: + - ".gitpod.yml" + short_description: "Include a gitpod environment" + description: "Include the configuration required to use Gitpod." + help_text: | + Gitpod (https://www.gitpod.io/) provides standardized and automated development environments. + + Including this to your pipeline will provide an environment with the latest version of nf-core/tools installed and all its requirements. + This is useful to have all the tools ready for pipeline development. + nfcore_pipelines: False + custom_pipelines: True + default: true + + codespaces: + skippable_paths: + - ".devcontainer/devcontainer.json" + short_description: "Include GitHub Codespaces" + description: "The pipeline will include a devcontainer configuration for GitHub Codespaces, providing a development environment with nf-core/tools and Nextflow installed." + help_text: | + The pipeline will include a devcontainer configuration. + The devcontainer will create a GitHub Codespaces for Nextflow development with nf-core/tools and Nextflow installed. + + Github Codespaces (https://github.com/features/codespaces) is an online developer environment that runs in your browser, complete with VSCode and a terminal. + linting: + files_unchanged: + - ".github/CONTRIBUTING.md" + nfcore_pipelines: False + custom_pipelines: True + default: true + + vscode: + skippable_paths: + - ".vscode" + short_description: "Render website admonitions in VSCode" + description: "Add a VSCode configuration to render website admonitions" + help_text: | + This will add a VSCode configuration file to render the admonitions in markdown files with the same style as the nf-core website. + + Adds the `.vscode` directory to the pipelinerepository. + nfcore_pipelines: False + custom_pipelines: True + default: true + +code_quality: + name: "Code Quality" + features: + code_linters: + skippable_paths: + - ".pre-commit-config.yaml" + - ".prettierignore" + - ".prettierrc.yml" + - ".github/workflows/fix-linting.yml" + short_description: "Use code linters" + description: "The pipeline will include code linters and CI tests to lint your code: pre-commit, editor-config and prettier." + help_text: | + Pipelines include code linters to check the formatting of your code in order to harmonize code styles between developers. + Linters will check all non-ignored files, e.g., JSON, YAML, Nextlow or Python files in your repository. + The available code linters are: + + - pre-commit (https://pre-commit.com/): used to run all code-linters on every PR and on ever commit if you run `pre-commit install` to install it in your local repository. + - prettier (https://github.com/prettier/prettier): enforces a consistent style (indentation, quoting, line length, etc). + linting: + files_exist: + - ".prettierignore" + - ".prettierrc.yml" + nfcore_pipelines: False + custom_pipelines: True + default: true + +documentation_metadata: + name: "Documentation & metadata" + features: + citations: + skippable_paths: + - "assets/methods_description_template.yml" + - "CITATIONS.md" + short_description: "Include citations" + description: "Include pipeline tools citations in CITATIONS.md and a method description in the MultiQC report (if enabled)." + help_text: | + If adding citations, the pipeline template will contain a `CITATIONS.md` file to add the citations of all tools used in the pipeline. + + Additionally, it will include a YAML file (`assets/methods_description_template.yml`) to add a Materials & Methods section describing the tools used in the pieline, + and the logics to add this section to the output MultiQC report (if the report is generated). + linting: + files_exist: + - "CITATIONS.md" + nfcore_pipelines: False + custom_pipelines: True + default: true + + documentation: + skippable_paths: + - "docs" + short_description: "Add documentation" + description: "Add documentation to the pipeline" + help_text: | + This will add documentation markdown files where you can describe your pipeline. + It includes: + - docs/README.md: A README file where you can describe the structure of your documentation. + - docs/output.md: A file where you can explain the output generated by the pipeline + - docs/usage.md: A file where you can explain the usage of the pipeline and its parameters. + + These files come with an exemplary documentation structure written. + linting: + files_exist: + - "docs/output.md" + - "docs/README.md" + - "docs/usage.md" + nfcore_pipelines: False + custom_pipelines: True + default: true + + rocrate: + skippable_paths: + - "ro-crate-metadata.json" + short_description: "Add RO-Crate metadata" + description: "Add a RO-Crate metadata file to describe the pipeline" + help_text: | + RO-Crate is a metadata specification to describe research data and software. + This will add a `ro-crate-metadata.json` file to describe the pipeline. + nfcore_pipelines: False + custom_pipelines: True + linting: + files_warn: + - "ro-crate-metadata.json" + files_unchanged: + - ".prettierignore" + default: true + +notifications: + name: "Notifications" + features: + email: + skippable_paths: + - "assets/email_template.html" + - "assets/sendmail_template.txt" + - "assets/email_template.txt" + short_description: "Enable email updates" + description: "Enable sending emails on pipeline completion." + help_text: | + Enable the option of sending an email which will include pipeline execution reports on pipeline completion. + linting: + files_exist: + - "assets/email_template.html" + - "assets/sendmail_template.txt" + - "assets/email_template.txt" + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True + default: true + + adaptivecard: + skippable_paths: + - "assets/adaptivecard.json" + short_description: "Support Microsoft Teams notifications" + description: "Enable pipeline status update messages through Microsoft Teams" + help_text: | + This adds an Adaptive Card. A snippets of user interface. + This Adaptive Card is used as a template for pipeline update messages and it is compatible with Microsoft Teams. + linting: + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True + default: true + + slackreport: + skippable_paths: + - "assets/slackreport.json" + short_description: "Support Slack notifications" + description: "Enable pipeline status update messages through Slack" + help_text: | + This adds an JSON template used as a template for pipeline update messages in Slack. + linting: + files_unchanged: + - ".prettierignore" + nfcore_pipelines: False + custom_pipelines: True + default: true From 0cf08ba9e3df9cc805e2cb0b2bad25215ea2b3bf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 12:01:36 +0200 Subject: [PATCH 10/33] update yq command to read new template_features.yml structure --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 8c025f5f97..4dfc40a73c 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -38,7 +38,7 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq 'keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT + echo "matrix=$(yq ' .[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | .[] | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: From c5cefe50c9b9c67f0bceea4725b2dea98a4f7224 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 12:10:36 +0200 Subject: [PATCH 11/33] update tests accessing template_features.yml --- nf_core/pipelines/create/create.py | 43 +++++++++++++++++------------- tests/pipelines/test_create.py | 11 +++++--- 2 files changed, 32 insertions(+), 22 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index a370ee2391..076a971cb2 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -112,7 +112,12 @@ def __init__( self.template_features_yml = yaml.safe_load(rendered_features) # Get list of files we're skipping with the supplied skip keys - self.skip_paths = set(sp for k in self.skip_areas for sp in self.template_features_yml[k]["skippable_paths"]) + skip_paths: list = [] + for section in self.template_features_yml.values(): + for feature in section["features"].values(): + if feature["skippable_paths"]: + skip_paths = skip_paths + feature["skippable_paths"] + self.skip_paths = set(skip_paths) # Set convenience variables self.name = self.config.name @@ -214,13 +219,14 @@ def obtain_jinja_params_dict( # Add template areas to jinja params and create list of areas with paths to skip skip_areas = [] - for t_area in self.template_features_yml.keys(): - if t_area in features_to_skip: - if self.template_features_yml[t_area]["skippable_paths"]: - skip_areas.append(t_area) - jinja_params[t_area] = False - else: - jinja_params[t_area] = True + for section in self.template_features_yml.values(): + for t_area in section["features"].keys(): + if t_area in features_to_skip: + if section["features"][t_area]["skippable_paths"]: + skip_areas.append(t_area) + jinja_params[t_area] = False + else: + jinja_params[t_area] = True # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files if not self.config.is_nfcore: @@ -399,16 +405,17 @@ def fix_linting(self): lint_config = {} for area in (self.config.skip_features or []) + self.skip_areas: try: - for lint_test in self.template_features_yml[area]["linting"]: - try: - if self.template_features_yml[area]["linting"][lint_test]: - lint_config.setdefault(lint_test, []).extend( - self.template_features_yml[area]["linting"][lint_test] - ) - else: - lint_config[lint_test] = False - except AttributeError: - pass # When linting is False + for section in self.template_features_yml.values(): + for lint_test in section["features"][area]["linting"]: + try: + if section["features"][area]["linting"][lint_test]: + lint_config.setdefault(lint_test, []).extend( + section["features"][area]["linting"][lint_test] + ) + else: + lint_config[lint_test] = False + except AttributeError: + pass # When linting is False except KeyError: pass # Areas without linting diff --git a/tests/pipelines/test_create.py b/tests/pipelines/test_create.py index b8e8cb22a2..d2ee4dd246 100644 --- a/tests/pipelines/test_create.py +++ b/tests/pipelines/test_create.py @@ -104,7 +104,9 @@ def test_pipeline_creation_initiation_customize_template(self, tmp_path): def test_pipeline_creation_with_yml_skip(self, tmp_path): # Update pipeline_create_template_skip.yml file template_features_yml = load_features_yaml() - all_features = list(template_features_yml.keys()) + all_features = [] + for section in template_features_yml.values(): + all_features += list(section["features"].keys()) all_features.remove("is_nfcore") env = jinja2.Environment(loader=jinja2.PackageLoader("tests", "data"), keep_trailing_newline=True) skip_template = env.get_template( @@ -148,9 +150,10 @@ def test_template_customisation_all_files_grouping(self): "workflows/pipeline.nf", ] all_skipped_files = [] - for feature in template_features_yml.keys(): - if template_features_yml[feature]["skippable_paths"]: - all_skipped_files.extend(template_features_yml[feature]["skippable_paths"]) + for section in template_features_yml.values(): + for feature in section["features"].keys(): + if section["features"][feature]["skippable_paths"]: + all_skipped_files.extend(section["features"][feature]["skippable_paths"]) for root, _, files in os.walk(PIPELINE_TEMPLATE): for file in files: From f40bb9edf275a61047541e80b0e5e07f4b663296 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 13:08:10 +0200 Subject: [PATCH 12/33] fix yq command --- .github/workflows/create-test-lint-wf-template.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 4dfc40a73c..8e4e633ddb 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -38,7 +38,8 @@ jobs: - name: Create Matrix id: create_matrix run: | - echo "matrix=$(yq ' .[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config") | .[] | tojson(0)' nf_core/pipelines/create/template_features.yml)" >> $GITHUB_OUTPUT + echo "matrix=$(yq '.[].features | keys | filter(. != "github") | filter(. != "is_nfcore") | filter(. != "test_config")' nf_core/pipelines/create/template_features.yml | \ + yq 'flatten | tojson(0)' -)" >> $GITHUB_OUTPUT RunTestWorkflow: runs-on: From fa45b84046f27db754e93bfe099fa9dd584380e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 16:10:24 +0200 Subject: [PATCH 13/33] fix getting skip paths --- nf_core/pipelines/create/create.py | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 076a971cb2..980f5eaf71 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -112,11 +112,13 @@ def __init__( self.template_features_yml = yaml.safe_load(rendered_features) # Get list of files we're skipping with the supplied skip keys + skip_paths: list = [] - for section in self.template_features_yml.values(): - for feature in section["features"].values(): - if feature["skippable_paths"]: - skip_paths = skip_paths + feature["skippable_paths"] + for feature in self.skip_areas: + for section in self.template_features_yml.values(): + if feature in section["features"]: + if section["features"][feature]["skippable_paths"]: + skip_paths = skip_paths + section["features"][feature]["skippable_paths"] self.skip_paths = set(skip_paths) # Set convenience variables From 56287e8194a2675fdc17d4dfa072f4e1ec73ac94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 16:47:54 +0200 Subject: [PATCH 14/33] fix lint_config --- nf_core/pipelines/create/create.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 980f5eaf71..a2566b6a34 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -407,12 +407,12 @@ def fix_linting(self): lint_config = {} for area in (self.config.skip_features or []) + self.skip_areas: try: - for section in self.template_features_yml.values(): - for lint_test in section["features"][area]["linting"]: + for section_name in self.template_features_yml.keys(): + for lint_test in self.template_features_yml[section_name]["features"][area]["linting"]: try: - if section["features"][area]["linting"][lint_test]: + if self.template_features_yml[section_name]["features"][area]["linting"][lint_test]: lint_config.setdefault(lint_test, []).extend( - section["features"][area]["linting"][lint_test] + self.template_features_yml[section_name]["features"][area]["linting"][lint_test] ) else: lint_config[lint_test] = False From db16ba95dcf34c27f0159d498405f3ab86152c9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 25 Jun 2025 17:13:47 +0200 Subject: [PATCH 15/33] fix linting config again --- nf_core/pipelines/create/create.py | 22 ++++++++++++---------- 1 file changed, 12 insertions(+), 10 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index a2566b6a34..4b7bfd46c0 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -405,19 +405,21 @@ def fix_linting(self): """ # Create a lint config lint_config = {} + print((self.config.skip_features or []) + self.skip_areas) for area in (self.config.skip_features or []) + self.skip_areas: try: for section_name in self.template_features_yml.keys(): - for lint_test in self.template_features_yml[section_name]["features"][area]["linting"]: - try: - if self.template_features_yml[section_name]["features"][area]["linting"][lint_test]: - lint_config.setdefault(lint_test, []).extend( - self.template_features_yml[section_name]["features"][area]["linting"][lint_test] - ) - else: - lint_config[lint_test] = False - except AttributeError: - pass # When linting is False + if area in self.template_features_yml[section_name]["features"]: + for lint_test in self.template_features_yml[section_name]["features"][area]["linting"]: + try: + if self.template_features_yml[section_name]["features"][area]["linting"][lint_test]: + lint_config.setdefault(lint_test, []).extend( + self.template_features_yml[section_name]["features"][area]["linting"][lint_test] + ) + else: + lint_config[lint_test] = False + except AttributeError: + pass # When linting is False except KeyError: pass # Areas without linting From 96ad11442808d2a93cd4ee704025c6efd8eaa395 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 09:38:52 +0200 Subject: [PATCH 16/33] fix nf-test linting when nf-test is skipped --- nf_core/pipelines/create/create.py | 3 +- .../pipelines/create/template_features.yml | 1 + nf_core/pipelines/lint/nf_test_content.py | 69 ++++++++++--------- 3 files changed, 38 insertions(+), 35 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 4b7bfd46c0..9ef431dfcb 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -405,8 +405,7 @@ def fix_linting(self): """ # Create a lint config lint_config = {} - print((self.config.skip_features or []) + self.skip_areas) - for area in (self.config.skip_features or []) + self.skip_areas: + for area in set((self.config.skip_features or []) + self.skip_areas): try: for section_name in self.template_features_yml.keys(): if area in self.template_features_yml[section_name]["features"]: diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 76b6857365..f052ac6e5b 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -185,6 +185,7 @@ continuous_integration_testing: - ".github/actions/nf-test/action.yml" - "nf-test.config" - "tests/default.nf.test" + nf_test_content: False nfcore_pipelines: False custom_pipelines: True default: true diff --git a/nf_core/pipelines/lint/nf_test_content.py b/nf_core/pipelines/lint/nf_test_content.py index edea8c8b5f..70f5bc1a21 100644 --- a/nf_core/pipelines/lint/nf_test_content.py +++ b/nf_core/pipelines/lint/nf_test_content.py @@ -144,25 +144,25 @@ def nf_test_content(self) -> dict[str, list[str]]: # Check if tests/nextflow.config is present if not conf_fn.exists(): failed.append(f"'{conf_fn.relative_to(self.wf_path)}' does not exist") - - if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: - checks_passed = {check: False for check in config_checks} - with open(conf_fn) as fh: - for line in fh: - line = line.strip() - for check_name, config_check_info in config_checks.items(): - if re.search(str(config_check_info["pattern"]), line): - passed.append( - f"'{conf_fn.relative_to(self.wf_path)}' contains {config_check_info['description']}" - ) - checks_passed[check_name] = True - for check_name, config_check_info in config_checks.items(): - if not checks_passed[check_name]: - failed.append( - f"'{conf_fn.relative_to(self.wf_path)}' does not contain {config_check_info['description']}" - ) else: - ignored.append(f"'{conf_fn.relative_to(self.wf_path)}' checking ignored") + if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: + checks_passed = {check: False for check in config_checks} + with open(conf_fn) as fh: + for line in fh: + line = line.strip() + for check_name, config_check_info in config_checks.items(): + if re.search(str(config_check_info["pattern"]), line): + passed.append( + f"'{conf_fn.relative_to(self.wf_path)}' contains {config_check_info['description']}" + ) + checks_passed[check_name] = True + for check_name, config_check_info in config_checks.items(): + if not checks_passed[check_name]: + failed.append( + f"'{conf_fn.relative_to(self.wf_path)}' does not contain {config_check_info['description']}" + ) + else: + ignored.append(f"'{conf_fn.relative_to(self.wf_path)}' checking ignored") # Content of nf-test.config file nf_test_conf_fn = Path(self.wf_path, "nf-test.config") @@ -184,21 +184,24 @@ def nf_test_content(self) -> dict[str, list[str]]: }, } - if nf_test_content_conf is None or str(nf_test_conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: - checks_passed = {check: False for check in nf_test_checks} - with open(nf_test_conf_fn) as fh: - for line in fh: - line = line.strip() - for check_name, nf_test_check_info in nf_test_checks.items(): - if re.search(str(nf_test_check_info["pattern"]), line): - passed.append( - f"'{nf_test_conf_fn.relative_to(self.wf_path)}' {nf_test_check_info['description']}" - ) - checks_passed[check_name] = True - for check_name, nf_test_check_info in nf_test_checks.items(): - if not checks_passed[check_name]: - failed.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' {nf_test_check_info['failure_msg']}") + if not nf_test_conf_fn.exists(): + failed.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' does not exist") else: - ignored.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' checking ignored") + if nf_test_content_conf is None or str(nf_test_conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf: + checks_passed = {check: False for check in nf_test_checks} + with open(nf_test_conf_fn) as fh: + for line in fh: + line = line.strip() + for check_name, nf_test_check_info in nf_test_checks.items(): + if re.search(str(nf_test_check_info["pattern"]), line): + passed.append( + f"'{nf_test_conf_fn.relative_to(self.wf_path)}' {nf_test_check_info['description']}" + ) + checks_passed[check_name] = True + for check_name, nf_test_check_info in nf_test_checks.items(): + if not checks_passed[check_name]: + failed.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' {nf_test_check_info['failure_msg']}") + else: + ignored.append(f"'{nf_test_conf_fn.relative_to(self.wf_path)}' checking ignored") return {"passed": passed, "failed": failed, "ignored": ignored} From 4a8540570717b3d51dca6bfcf5f4fd20871388d6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 10:02:08 +0200 Subject: [PATCH 17/33] fix nf-test snapshots for non nf-core pipelines --- .github/snapshots/adaptivecard.nf.test.snap | 9 ++++++++- .github/snapshots/changelog.nf.test.snap | 9 ++++++++- .github/snapshots/ci.nf.test.snap | 9 ++++++++- .github/snapshots/citations.nf.test.snap | 9 ++++++++- .github/snapshots/code_linters.nf.test.snap | 9 ++++++++- .github/snapshots/codespaces.nf.test.snap | 9 ++++++++- .github/snapshots/documentation.nf.test.snap | 9 ++++++++- .github/snapshots/email.nf.test.snap | 9 ++++++++- .github/snapshots/fastqc.nf.test.snap | 6 +++++- .github/snapshots/github_badges.nf.test.snap | 9 ++++++++- .github/snapshots/gitpod.nf.test.snap | 9 ++++++++- .github/snapshots/gpu.nf.test.snap | 2 +- .github/snapshots/igenomes.nf.test.snap | 9 ++++++++- .github/snapshots/license.nf.test.snap | 9 ++++++++- .github/snapshots/nf_core_configs.nf.test.snap | 9 ++++++++- .github/snapshots/nf_schema.nf.test.snap | 9 ++++++++- .github/snapshots/rocrate.nf.test.snap | 9 ++++++++- .github/snapshots/seqera_platform.nf.test.snap | 9 ++++++++- .github/snapshots/slackreport.nf.test.snap | 9 ++++++++- .github/snapshots/vscode.nf.test.snap | 9 ++++++++- nf_core/pipeline-template/tests/default.nf.test | 2 +- 21 files changed, 151 insertions(+), 21 deletions(-) diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/adaptivecard.nf.test.snap +++ b/.github/snapshots/adaptivecard.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap index 8a5e05c858..3e3f66115d 100644 --- a/.github/snapshots/changelog.nf.test.snap +++ b/.github/snapshots/changelog.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap index ce4a455ac3..935c455840 100644 --- a/.github/snapshots/ci.nf.test.snap +++ b/.github/snapshots/ci.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap index 6d7cecc8b5..c4de783800 100644 --- a/.github/snapshots/citations.nf.test.snap +++ b/.github/snapshots/citations.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap index 6d7cecc8b5..c4de783800 100644 --- a/.github/snapshots/code_linters.nf.test.snap +++ b/.github/snapshots/code_linters.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap index 6d7cecc8b5..c4de783800 100644 --- a/.github/snapshots/codespaces.nf.test.snap +++ b/.github/snapshots/codespaces.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/documentation.nf.test.snap +++ b/.github/snapshots/documentation.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/email.nf.test.snap +++ b/.github/snapshots/email.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap index d91149e893..3397debb07 100644 --- a/.github/snapshots/fastqc.nf.test.snap +++ b/.github/snapshots/fastqc.nf.test.snap @@ -2,7 +2,11 @@ "-profile test": { "content": [ 1, - null, + { + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "multiqc", "multiqc/multiqc_data", diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap index cb8c64a661..5bce329494 100644 --- a/.github/snapshots/github_badges.nf.test.snap +++ b/.github/snapshots/github_badges.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap index 6d7cecc8b5..c4de783800 100644 --- a/.github/snapshots/gitpod.nf.test.snap +++ b/.github/snapshots/gitpod.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index b21a89180d..d77b96fad1 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -89,7 +89,7 @@ "multiqc/multiqc_plots/svg/general_stats_table.svg", "multiqc/multiqc_report.html", "pipeline_info", - "pipeline_info/nf_core_testpipeline_software_mqc_versions.yml" + "pipeline_info/testpipeline_software_mqc_versions.yml" ], [ "fastqc-status-check-heatmap.txt:md5,0f1975c565a16bf09be08a05c204ded7", diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap index 8ca4448ccd..6c750439a3 100644 --- a/.github/snapshots/igenomes.nf.test.snap +++ b/.github/snapshots/igenomes.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/license.nf.test.snap +++ b/.github/snapshots/license.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap index 6d7cecc8b5..c4de783800 100644 --- a/.github/snapshots/nf_core_configs.nf.test.snap +++ b/.github/snapshots/nf_core_configs.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap index d7a15c6252..c05cd336ec 100644 --- a/.github/snapshots/nf_schema.nf.test.snap +++ b/.github/snapshots/nf_schema.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/rocrate.nf.test.snap +++ b/.github/snapshots/rocrate.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/seqera_platform.nf.test.snap +++ b/.github/snapshots/seqera_platform.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/slackreport.nf.test.snap +++ b/.github/snapshots/slackreport.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap index 3ee6132d83..232f6b2e14 100644 --- a/.github/snapshots/vscode.nf.test.snap +++ b/.github/snapshots/vscode.nf.test.snap @@ -2,7 +2,14 @@ "-profile test": { "content": [ 4, - null, + { + "FASTQC": { + "fastqc": "0.12.1" + }, + "Workflow": { + "nf-core/testpipeline": "v1.0.0dev" + } + }, [ "fastqc", "fastqc/SAMPLE1_PE_1_fastqc.html", diff --git a/nf_core/pipeline-template/tests/default.nf.test b/nf_core/pipeline-template/tests/default.nf.test index d0fe324a3a..a2eba5a782 100644 --- a/nf_core/pipeline-template/tests/default.nf.test +++ b/nf_core/pipeline-template/tests/default.nf.test @@ -23,7 +23,7 @@ nextflow_pipeline { // Number of successful tasks workflow.trace.succeeded().size(), // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions - removeNextflowVersion("$outputDir/pipeline_info/nf_core_{{ short_name }}_software_mqc_versions.yml"), + removeNextflowVersion("$outputDir/pipeline_info/{% if is_nfcore %}nf_core_{% endif %}{{ short_name }}_software_mqc_versions.yml"), // All stable path name, with a relative path stable_name, // All files with stable contents From 157ed0953126e89d7c3fa6c9f50984594283ccda Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 10:12:16 +0200 Subject: [PATCH 18/33] more test snapshots fixes --- .github/snapshots/changelog.nf.test.snap | 2 +- .github/snapshots/ci.nf.test.snap | 2 +- .github/snapshots/citations.nf.test.snap | 2 +- .github/snapshots/code_linters.nf.test.snap | 2 +- .github/snapshots/codespaces.nf.test.snap | 2 +- .github/snapshots/default.nf.test.snap | 2 +- .github/snapshots/documentation.nf.test.snap | 2 +- .github/snapshots/email.nf.test.snap | 2 +- .github/snapshots/fastqc.nf.test.snap | 2 +- .github/snapshots/github_badges.nf.test.snap | 2 +- .github/snapshots/gitpod.nf.test.snap | 2 +- .github/snapshots/gpu.nf.test.snap | 2 +- .github/snapshots/igenomes.nf.test.snap | 2 +- .github/snapshots/license.nf.test.snap | 2 +- .github/snapshots/nf_core_configs.nf.test.snap | 2 +- .github/snapshots/nf_schema.nf.test.snap | 2 +- .github/snapshots/rocrate.nf.test.snap | 2 +- .github/snapshots/seqera_platform.nf.test.snap | 2 +- .github/snapshots/slackreport.nf.test.snap | 2 +- .github/snapshots/vscode.nf.test.snap | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/.github/snapshots/changelog.nf.test.snap b/.github/snapshots/changelog.nf.test.snap index 3e3f66115d..98b73b4779 100644 --- a/.github/snapshots/changelog.nf.test.snap +++ b/.github/snapshots/changelog.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/ci.nf.test.snap b/.github/snapshots/ci.nf.test.snap index 935c455840..61b7b49132 100644 --- a/.github/snapshots/ci.nf.test.snap +++ b/.github/snapshots/ci.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/citations.nf.test.snap b/.github/snapshots/citations.nf.test.snap index c4de783800..fcf055e0cc 100644 --- a/.github/snapshots/citations.nf.test.snap +++ b/.github/snapshots/citations.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/code_linters.nf.test.snap b/.github/snapshots/code_linters.nf.test.snap index c4de783800..fcf055e0cc 100644 --- a/.github/snapshots/code_linters.nf.test.snap +++ b/.github/snapshots/code_linters.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/codespaces.nf.test.snap b/.github/snapshots/codespaces.nf.test.snap index c4de783800..fcf055e0cc 100644 --- a/.github/snapshots/codespaces.nf.test.snap +++ b/.github/snapshots/codespaces.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index baa9ba23cb..6f55416ec5 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/documentation.nf.test.snap b/.github/snapshots/documentation.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/documentation.nf.test.snap +++ b/.github/snapshots/documentation.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/email.nf.test.snap b/.github/snapshots/email.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/email.nf.test.snap +++ b/.github/snapshots/email.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/fastqc.nf.test.snap b/.github/snapshots/fastqc.nf.test.snap index 3397debb07..5ce3dec844 100644 --- a/.github/snapshots/fastqc.nf.test.snap +++ b/.github/snapshots/fastqc.nf.test.snap @@ -4,7 +4,7 @@ 1, { "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/github_badges.nf.test.snap b/.github/snapshots/github_badges.nf.test.snap index 5bce329494..ed83e9a3a7 100644 --- a/.github/snapshots/github_badges.nf.test.snap +++ b/.github/snapshots/github_badges.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/gitpod.nf.test.snap b/.github/snapshots/gitpod.nf.test.snap index c4de783800..fcf055e0cc 100644 --- a/.github/snapshots/gitpod.nf.test.snap +++ b/.github/snapshots/gitpod.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index d77b96fad1..eb56c28c62 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/igenomes.nf.test.snap b/.github/snapshots/igenomes.nf.test.snap index 6c750439a3..ce01d9d5d4 100644 --- a/.github/snapshots/igenomes.nf.test.snap +++ b/.github/snapshots/igenomes.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/license.nf.test.snap b/.github/snapshots/license.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/license.nf.test.snap +++ b/.github/snapshots/license.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/nf_core_configs.nf.test.snap b/.github/snapshots/nf_core_configs.nf.test.snap index c4de783800..fcf055e0cc 100644 --- a/.github/snapshots/nf_core_configs.nf.test.snap +++ b/.github/snapshots/nf_core_configs.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/nf_schema.nf.test.snap b/.github/snapshots/nf_schema.nf.test.snap index c05cd336ec..bd6eb4e0cf 100644 --- a/.github/snapshots/nf_schema.nf.test.snap +++ b/.github/snapshots/nf_schema.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/rocrate.nf.test.snap b/.github/snapshots/rocrate.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/rocrate.nf.test.snap +++ b/.github/snapshots/rocrate.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/seqera_platform.nf.test.snap b/.github/snapshots/seqera_platform.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/seqera_platform.nf.test.snap +++ b/.github/snapshots/seqera_platform.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/slackreport.nf.test.snap b/.github/snapshots/slackreport.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/slackreport.nf.test.snap +++ b/.github/snapshots/slackreport.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/vscode.nf.test.snap b/.github/snapshots/vscode.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/vscode.nf.test.snap +++ b/.github/snapshots/vscode.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ From 0aafacffc97c317d9d6101d3dac5a3a6c13cc11f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 10:18:54 +0200 Subject: [PATCH 19/33] last pipeline test snapshot fixes --- .github/snapshots/adaptivecard.nf.test.snap | 2 +- .github/snapshots/default.nf.test.snap | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/snapshots/adaptivecard.nf.test.snap b/.github/snapshots/adaptivecard.nf.test.snap index 232f6b2e14..8de215fd4e 100644 --- a/.github/snapshots/adaptivecard.nf.test.snap +++ b/.github/snapshots/adaptivecard.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "nf-core/testpipeline": "v1.0.0dev" + "my-prefix/testpipeline": "v1.0.0dev" } }, [ diff --git a/.github/snapshots/default.nf.test.snap b/.github/snapshots/default.nf.test.snap index 6f55416ec5..baa9ba23cb 100644 --- a/.github/snapshots/default.nf.test.snap +++ b/.github/snapshots/default.nf.test.snap @@ -7,7 +7,7 @@ "fastqc": "0.12.1" }, "Workflow": { - "my-prefix/testpipeline": "v1.0.0dev" + "nf-core/testpipeline": "v1.0.0dev" } }, [ From f6c1395e74daabc5bf59aba8a3a3de2b00ad4fee Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 10:27:54 +0200 Subject: [PATCH 20/33] update pytest snapshots --- .../test_basic_details_custom.svg | 246 ++++++++--------- .../test_basic_details_nfcore.svg | 254 ++++++++--------- .../test_create_app/test_choose_type.svg | 246 ++++++++--------- .../test_customisation_help.svg | 261 +++++++++--------- .../test_create_app/test_final_details.svg | 242 ++++++++-------- .../test_create_app/test_github_details.svg | 258 ++++++++--------- .../test_github_exit_message.svg | 247 +++++++++-------- .../test_create_app/test_github_question.svg | 236 ++++++++-------- .../test_create_app/test_type_custom.svg | 256 +++++++++-------- .../test_create_app/test_type_nfcore.svg | 252 +++++++++-------- .../test_type_nfcore_validation.svg | 252 ++++++++--------- .../test_create_app/test_welcome.svg | 243 ++++++++-------- tests/pipelines/test_create_app.py | 2 +- 13 files changed, 1494 insertions(+), 1501 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 3d74d0761e..d50fefd129 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1771001981-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1771001981-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #191919 } -.terminal-r9 { fill: #737373 } -.terminal-r10 { fill: #b93c5b } -.terminal-r11 { fill: #2d2d2d } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #e0e0e0;font-weight: bold } -.terminal-r14 { fill: #0a180e;font-weight: bold } -.terminal-r15 { fill: #0d0d0d } -.terminal-r16 { fill: #495259 } -.terminal-r17 { fill: #ffa62b;font-weight: bold } + .terminal-1771001981-r1 { fill: #c5c8c6 } +.terminal-1771001981-r2 { fill: #e0e0e0 } +.terminal-1771001981-r3 { fill: #94999c } +.terminal-1771001981-r4 { fill: #0178d4;font-weight: bold } +.terminal-1771001981-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-1771001981-r6 { fill: #121212 } +.terminal-1771001981-r7 { fill: #008139 } +.terminal-1771001981-r8 { fill: #191919 } +.terminal-1771001981-r9 { fill: #737373 } +.terminal-1771001981-r10 { fill: #b93c5b } +.terminal-1771001981-r11 { fill: #2d2d2d } +.terminal-1771001981-r12 { fill: #7ae998 } +.terminal-1771001981-r13 { fill: #e0e0e0;font-weight: bold } +.terminal-1771001981-r14 { fill: #0a180e;font-weight: bold } +.terminal-1771001981-r15 { fill: #0d0d0d } +.terminal-1771001981-r16 { fill: #495259 } +.terminal-1771001981-r17 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 8ccef7d421..afe90752e7 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3122270943-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3122270943-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #084724 } -.terminal-r8 { fill: #0178d4 } -.terminal-r9 { fill: #a2a2a2 } -.terminal-r10 { fill: #797979 } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #191919 } -.terminal-r13 { fill: #737373 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #7ae998 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0a180e;font-weight: bold } -.terminal-r18 { fill: #0d0d0d } -.terminal-r19 { fill: #008139 } -.terminal-r20 { fill: #495259 } -.terminal-r21 { fill: #ffa62b;font-weight: bold } + .terminal-3122270943-r1 { fill: #c5c8c6 } +.terminal-3122270943-r2 { fill: #e0e0e0 } +.terminal-3122270943-r3 { fill: #94999c } +.terminal-3122270943-r4 { fill: #0178d4;font-weight: bold } +.terminal-3122270943-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-3122270943-r6 { fill: #121212 } +.terminal-3122270943-r7 { fill: #084724 } +.terminal-3122270943-r8 { fill: #0178d4 } +.terminal-3122270943-r9 { fill: #a2a2a2 } +.terminal-3122270943-r10 { fill: #797979 } +.terminal-3122270943-r11 { fill: #b93c5b } +.terminal-3122270943-r12 { fill: #191919 } +.terminal-3122270943-r13 { fill: #737373 } +.terminal-3122270943-r14 { fill: #2d2d2d } +.terminal-3122270943-r15 { fill: #7ae998 } +.terminal-3122270943-r16 { fill: #e0e0e0;font-weight: bold } +.terminal-3122270943-r17 { fill: #0a180e;font-weight: bold } +.terminal-3122270943-r18 { fill: #0d0d0d } +.terminal-3122270943-r19 { fill: #008139 } +.terminal-3122270943-r20 { fill: #495259 } +.terminal-3122270943-r21 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 8c7c257684..13b727a372 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3499146822-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3499146822-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #0178d4;text-decoration: underline; } -.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } -.terminal-r7 { fill: #e1e1e1;font-weight: bold } -.terminal-r8 { fill: #e0e0e0;font-style: italic; } -.terminal-r9 { fill: #7ae998 } -.terminal-r10 { fill: #6db2ff } -.terminal-r11 { fill: #55c076;font-weight: bold } -.terminal-r12 { fill: #ddedf9;font-weight: bold } -.terminal-r13 { fill: #008139 } -.terminal-r14 { fill: #004295 } -.terminal-r15 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r16 { fill: #ffa62b;font-weight: bold } -.terminal-r17 { fill: #495259 } + .terminal-3499146822-r1 { fill: #c5c8c6 } +.terminal-3499146822-r2 { fill: #e0e0e0 } +.terminal-3499146822-r3 { fill: #94999c } +.terminal-3499146822-r4 { fill: #0178d4;font-weight: bold } +.terminal-3499146822-r5 { fill: #0178d4;text-decoration: underline; } +.terminal-3499146822-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } +.terminal-3499146822-r7 { fill: #4ebf71;font-weight: bold } +.terminal-3499146822-r8 { fill: #e0e0e0;font-style: italic; } +.terminal-3499146822-r9 { fill: #7ae998 } +.terminal-3499146822-r10 { fill: #6db2ff } +.terminal-3499146822-r11 { fill: #55c076;font-weight: bold } +.terminal-3499146822-r12 { fill: #ddedf9;font-weight: bold } +.terminal-3499146822-r13 { fill: #008139 } +.terminal-3499146822-r14 { fill: #004295 } +.terminal-3499146822-r15 { fill: #e1e1e1;text-decoration: underline; } +.terminal-3499146822-r16 { fill: #ffa62b;font-weight: bold } +.terminal-3499146822-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the● Your pipeline will never be part of nf-core -nf-core community● You want full control over all features that -● You think that there's an outside chanceare included from the template (including -that it ever could be part of nf-corethose that are mandatory for nf-core). - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the ● Your pipeline will never be part of nf-core +nf-core community● You want full control over all features that +● You think that there's an outside chance are included from the template (including  +that it ever could be part of nf-corethose that are mandatory for nf-core). + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 15357a8674..3549e5e09f 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,259 +19,258 @@ font-weight: 700; } - .terminal-1435926941-matrix { + .terminal-682353586-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1435926941-title { + 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+.terminal-682353586-r23 { fill: #ffa62b;font-weight: bold } +.terminal-682353586-r24 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous▂▂ -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Hide help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - - -Nf-core pipelines are configured to use a copy of the most common reference -genome files. - -By selecting this option, your pipeline will include a configuration file -specifying the paths to these files. - -The required code to use these files will also be included in the template. When -the pipeline user provides an appropriate genome key, the pipeline will -automatically download the required reference files. -▅▅ -For more information about reference genomes in nf-core pipelines, see the - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette - + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. +▅▅ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of  Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +Continuous Integration & Testing + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index 3e0fe54057..c04d611ef6 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,249 +19,249 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3673759274-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3673759274-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #b93c5b } -.terminal-r9 { fill: #2d2d2d } -.terminal-r10 { fill: 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- + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Final details - - - - -First version of the pipelinePath to the output directory where the -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Final details + + + + +First version of the pipelinePath to the output directory where the  +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 6c83c1497b..823cc7827e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-matrix { + .terminal-4250860474-matrix { font-family: Fira Code, monospace; font-size: 20px; 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fill: #ddedf9;font-weight: bold } +.terminal-4250860474-r21 { fill: #004295 } +.terminal-4250860474-r22 { fill: #495259 } +.terminal-4250860474-r23 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - -Now that we have created a new pipeline locally, we can create a new GitHub repository and push -the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -The name of the organisation where theThe name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Create GitHub repository + +Now that we have created a new pipeline locally, we can create a new GitHub repository and push  +the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +The name of the organisation where the The name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user  +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index f28631fc53..54a14534cb 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,252 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-167342788-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-167342788-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #008000 } -.terminal-r6 { fill: #0000ff } -.terminal-r7 { fill: #ffff00 } -.terminal-r8 { fill: #e1e1e1;font-weight: bold } -.terminal-r9 { fill: #d2d2d2 } -.terminal-r10 { fill: #82aaff } -.terminal-r11 { fill: #eeffff } -.terminal-r12 { fill: #0f4b79 } -.terminal-r13 { fill: #a0a0a0;font-weight: bold } -.terminal-r14 { fill: #7ae998 } -.terminal-r15 { fill: #55c076;font-weight: bold } -.terminal-r16 { fill: #008139 } -.terminal-r17 { fill: #ffa62b;font-weight: bold } -.terminal-r18 { fill: #495259 } + .terminal-167342788-r1 { fill: #c5c8c6 } +.terminal-167342788-r2 { fill: #e0e0e0 } +.terminal-167342788-r3 { fill: #94999c } +.terminal-167342788-r4 { fill: #0178d4;font-weight: bold } +.terminal-167342788-r5 { fill: #008000 } +.terminal-167342788-r6 { fill: #ffff00 } +.terminal-167342788-r7 { fill: #4ebf71;font-weight: bold } +.terminal-167342788-r8 { fill: #d2d2d2 } +.terminal-167342788-r9 { fill: #82aaff } +.terminal-167342788-r10 { fill: #eeffff } +.terminal-167342788-r11 { fill: #18954b } +.terminal-167342788-r12 { fill: #959595;font-weight: bold } +.terminal-167342788-r13 { fill: #7ae998 } +.terminal-167342788-r14 { fill: #55c076;font-weight: bold } +.terminal-167342788-r15 { fill: #008139 } +.terminal-167342788-r16 { fill: #ffa62b;font-weight: bold } +.terminal-167342788-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -If you would like to create the GitHub repository later, you can do it manually by following -these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +If you would like to create the GitHub repository later, you can do it manually by following  +these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 77494c0bfe..8847cc9021 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,246 +19,246 @@ font-weight: 700; } - .terminal-matrix { + .terminal-309664288-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-309664288-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: 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- + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - - -After creating the pipeline template locally, we can create a GitHub repository and push the -code to it. - -Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Create GitHub repository + + +After creating the pipeline template locally, we can create a GitHub repository and push the  +code to it. + +Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 2e5f3497c2..20f874c94f 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,257 +19,255 @@ font-weight: 700; } - .terminal-3616702486-matrix { + .terminal-3243908447-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3616702486-title { + .terminal-3243908447-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #0178d4 } -.terminal-r7 { fill: #272727 } -.terminal-r8 { fill: #191919 } -.terminal-r9 { fill: #6db2ff } -.terminal-r10 { fill: #1e1e1e } -.terminal-r11 { fill: #808080 } -.terminal-r12 { fill: #ddedf9;font-weight: bold } -.terminal-r13 { fill: #004295 } -.terminal-r14 { fill: #000000 } -.terminal-r15 { fill: #2d2d2d } -.terminal-r16 { fill: #7ae998 } -.terminal-r17 { fill: #e0e0e0;font-weight: bold } -.terminal-r18 { fill: #0a180e;font-weight: bold } -.terminal-r19 { fill: #0d0d0d } -.terminal-r20 { fill: #008139 } -.terminal-r21 { fill: #ffa62b;font-weight: bold } -.terminal-r22 { fill: #495259 } - + .terminal-3243908447-r1 { fill: #c5c8c6 } +.terminal-3243908447-r2 { fill: #e0e0e0 } +.terminal-3243908447-r3 { fill: #94999c } +.terminal-3243908447-r4 { fill: #0178d4;font-weight: bold } +.terminal-3243908447-r5 { fill: #121212 } +.terminal-3243908447-r6 { fill: #0178d4 } +.terminal-3243908447-r7 { fill: #272727 } +.terminal-3243908447-r8 { fill: #191919 } +.terminal-3243908447-r9 { fill: #6db2ff } +.terminal-3243908447-r10 { fill: #1e1e1e } +.terminal-3243908447-r11 { fill: #808080 } +.terminal-3243908447-r12 { fill: #ddedf9;font-weight: bold } +.terminal-3243908447-r13 { fill: #004295 } +.terminal-3243908447-r14 { fill: #2d2d2d } +.terminal-3243908447-r15 { fill: #7ae998 } +.terminal-3243908447-r16 { fill: #e0e0e0;font-weight: bold } +.terminal-3243908447-r17 { fill: #0a180e;font-weight: bold } +.terminal-3243908447-r18 { fill: #0d0d0d } +.terminal-3243908447-r19 { fill: #008139 } +.terminal-3243908447-r20 { fill: #ffa62b;font-weight: bold } +.terminal-3243908447-r21 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) testing▃▃ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add configuration filesThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include configuration▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing -custom parameters -required to run nf-core -pipelines at different -institutions - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use code lintersThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include code linters and▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -CI tests to lint your -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub  Show help  +▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous  +Integration (CI) testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing  Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add pipeline testingAdd pipeline testing  Show help  +▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 39fcf40894..6c960fdc3f 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,255 +19,253 @@ font-weight: 700; } - - .terminal-matrix { + .terminal-201882774-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-201882774-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #191919 } -.terminal-r7 { fill: #6db2ff } -.terminal-r8 { fill: #1e1e1e } -.terminal-r9 { fill: #808080 } -.terminal-r10 { fill: #ddedf9;font-weight: bold } -.terminal-r11 { fill: #004295 } -.terminal-r12 { fill: #2d2d2d } 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+.terminal-201882774-r16 { fill: #0d0d0d } +.terminal-201882774-r17 { fill: #008139 } +.terminal-201882774-r18 { fill: #ffa62b;font-weight: bold } +.terminal-201882774-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - - - - - - - - - - - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Template features + + +Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a copy ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +of the most common  +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use multiqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the MultiQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +generates an HTML report  +for quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use fastqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the FastQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +performs quality control  +analysis of input FASTQ  +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use GPUAdd GPU support to the  Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 9c9f38bc80..2f80eff0d5 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-matrix { + .terminal-243002673-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-243002673-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #084724 } -.terminal-r8 { fill: #762b3d } -.terminal-r9 { fill: #a2a2a2 } -.terminal-r10 { fill: #737373 } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #2d2d2d } -.terminal-r13 { fill: #7ae998 } -.terminal-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-r15 { fill: #55c076;font-weight: bold } -.terminal-r16 { fill: #0d0d0d } -.terminal-r17 { fill: #008139 } -.terminal-r18 { fill: #ffa62b;font-weight: bold } -.terminal-r19 { fill: #495259 } + .terminal-243002673-r1 { fill: #c5c8c6 } +.terminal-243002673-r2 { fill: #e0e0e0 } +.terminal-243002673-r3 { fill: #94999c } +.terminal-243002673-r4 { fill: #0178d4;font-weight: bold } +.terminal-243002673-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-243002673-r6 { fill: #121212 } +.terminal-243002673-r7 { fill: #084724 } +.terminal-243002673-r8 { fill: #762b3d } +.terminal-243002673-r9 { fill: #a2a2a2 } +.terminal-243002673-r10 { fill: #737373 } +.terminal-243002673-r11 { fill: #b93c5b } +.terminal-243002673-r12 { fill: #2d2d2d } +.terminal-243002673-r13 { fill: #7ae998 } +.terminal-243002673-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-243002673-r15 { fill: #55c076;font-weight: bold } +.terminal-243002673-r16 { fill: #0d0d0d } +.terminal-243002673-r17 { fill: #008139 } +.terminal-243002673-r18 { fill: #ffa62b;font-weight: bold } +.terminal-243002673-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 875d7139cd..59698b22ef 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,250 +19,249 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1605040715-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1605040715-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #008000 } -.terminal-r5 { fill: #0000ff } -.terminal-r6 { fill: #ffff00 } -.terminal-r7 { fill: #0178d4;font-weight: bold } -.terminal-r8 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r9 { fill: #0f4b79 } -.terminal-r10 { fill: #e2e2e2;text-decoration: underline; } -.terminal-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #55c076;font-weight: bold } -.terminal-r14 { fill: #008139 } -.terminal-r15 { fill: #ffa62b;font-weight: bold } -.terminal-r16 { fill: #495259 } + .terminal-1605040715-r1 { fill: #c5c8c6 } +.terminal-1605040715-r2 { fill: #e0e0e0 } +.terminal-1605040715-r3 { fill: #94999c } +.terminal-1605040715-r4 { fill: #008000 } +.terminal-1605040715-r5 { fill: #ffff00 } +.terminal-1605040715-r6 { fill: #0178d4;font-weight: bold } +.terminal-1605040715-r7 { fill: #e1e1e1;text-decoration: underline; } +.terminal-1605040715-r8 { fill: #18954b } +.terminal-1605040715-r9 { fill: #e2e2e2;text-decoration: underline; } +.terminal-1605040715-r10 { fill: #e0e0e0;font-weight: bold;font-style: italic; } +.terminal-1605040715-r11 { fill: #7ae998 } +.terminal-1605040715-r12 { fill: #55c076;font-weight: bold } +.terminal-1605040715-r13 { fill: #008139 } +.terminal-1605040715-r14 { fill: #ffa62b;font-weight: bold } +.terminal-1605040715-r15 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core -pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core  +pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the  +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette diff --git a/tests/pipelines/test_create_app.py b/tests/pipelines/test_create_app.py index d87d016b3e..e359cc34e0 100644 --- a/tests/pipelines/test_create_app.py +++ b/tests/pipelines/test_create_app.py @@ -182,7 +182,7 @@ async def run_before(pilot) -> None: await pilot.press("tab") await pilot.press("M", "e") await pilot.click("#next") - await pilot.click("#igenomes") + await pilot.click("#github_badges") await pilot.press("tab") await pilot.press("enter") From 6714e08604b4398207c40cd72e2ac4dbdf9fc294 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 08:42:05 +0000 Subject: [PATCH 21/33] update pytest snapshots --- .../test_basic_details_custom.svg | 246 ++++++++--------- .../test_basic_details_nfcore.svg | 254 ++++++++--------- .../test_create_app/test_choose_type.svg | 246 ++++++++--------- .../test_customisation_help.svg | 260 +++++++++--------- .../test_create_app/test_final_details.svg | 242 ++++++++-------- .../test_create_app/test_github_details.svg | 258 ++++++++--------- .../test_github_exit_message.svg | 247 ++++++++--------- .../test_create_app/test_github_question.svg | 236 ++++++++-------- .../test_create_app/test_type_custom.svg | 254 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 250 ++++++++--------- .../test_type_nfcore_validation.svg | 250 ++++++++--------- .../test_create_app/test_welcome.svg | 243 ++++++++-------- 12 files changed, 1494 insertions(+), 1492 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index d50fefd129..3d74d0761e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-1771001981-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1771001981-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1771001981-r1 { fill: #c5c8c6 } -.terminal-1771001981-r2 { fill: #e0e0e0 } -.terminal-1771001981-r3 { fill: #94999c } -.terminal-1771001981-r4 { fill: #0178d4;font-weight: bold } -.terminal-1771001981-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-1771001981-r6 { fill: #121212 } -.terminal-1771001981-r7 { fill: #008139 } -.terminal-1771001981-r8 { fill: #191919 } -.terminal-1771001981-r9 { fill: #737373 } -.terminal-1771001981-r10 { fill: #b93c5b } -.terminal-1771001981-r11 { fill: #2d2d2d } -.terminal-1771001981-r12 { fill: #7ae998 } -.terminal-1771001981-r13 { fill: #e0e0e0;font-weight: bold } -.terminal-1771001981-r14 { fill: #0a180e;font-weight: bold } -.terminal-1771001981-r15 { fill: #0d0d0d } -.terminal-1771001981-r16 { fill: #495259 } -.terminal-1771001981-r17 { fill: #ffa62b;font-weight: bold } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #008139 } +.terminal-r8 { fill: #191919 } +.terminal-r9 { fill: #737373 } +.terminal-r10 { fill: #b93c5b } +.terminal-r11 { fill: #2d2d2d } +.terminal-r12 { fill: #7ae998 } +.terminal-r13 { fill: #e0e0e0;font-weight: bold } +.terminal-r14 { fill: #0a180e;font-weight: bold } +.terminal-r15 { fill: #0d0d0d } +.terminal-r16 { fill: #495259 } +.terminal-r17 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index afe90752e7..8ccef7d421 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-3122270943-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3122270943-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3122270943-r1 { fill: #c5c8c6 } -.terminal-3122270943-r2 { fill: #e0e0e0 } -.terminal-3122270943-r3 { fill: #94999c } -.terminal-3122270943-r4 { fill: #0178d4;font-weight: bold } -.terminal-3122270943-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-3122270943-r6 { fill: #121212 } -.terminal-3122270943-r7 { fill: #084724 } -.terminal-3122270943-r8 { fill: #0178d4 } -.terminal-3122270943-r9 { fill: #a2a2a2 } -.terminal-3122270943-r10 { fill: #797979 } -.terminal-3122270943-r11 { fill: #b93c5b } -.terminal-3122270943-r12 { fill: #191919 } -.terminal-3122270943-r13 { fill: #737373 } -.terminal-3122270943-r14 { fill: #2d2d2d } -.terminal-3122270943-r15 { fill: #7ae998 } -.terminal-3122270943-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-3122270943-r17 { fill: #0a180e;font-weight: bold } -.terminal-3122270943-r18 { fill: #0d0d0d } -.terminal-3122270943-r19 { fill: #008139 } -.terminal-3122270943-r20 { fill: #495259 } -.terminal-3122270943-r21 { 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+ - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 13b727a372..8c7c257684 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-3499146822-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3499146822-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3499146822-r1 { fill: #c5c8c6 } -.terminal-3499146822-r2 { fill: #e0e0e0 } -.terminal-3499146822-r3 { fill: #94999c } -.terminal-3499146822-r4 { fill: #0178d4;font-weight: bold } -.terminal-3499146822-r5 { fill: #0178d4;text-decoration: underline; } -.terminal-3499146822-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } -.terminal-3499146822-r7 { fill: #4ebf71;font-weight: bold } -.terminal-3499146822-r8 { fill: #e0e0e0;font-style: italic; } -.terminal-3499146822-r9 { fill: #7ae998 } -.terminal-3499146822-r10 { fill: #6db2ff } -.terminal-3499146822-r11 { fill: #55c076;font-weight: bold } -.terminal-3499146822-r12 { fill: #ddedf9;font-weight: bold } -.terminal-3499146822-r13 { fill: #008139 } -.terminal-3499146822-r14 { fill: #004295 } -.terminal-3499146822-r15 { fill: #e1e1e1;text-decoration: underline; } -.terminal-3499146822-r16 { fill: #ffa62b;font-weight: bold } -.terminal-3499146822-r17 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #0178d4;text-decoration: underline; } +.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } +.terminal-r7 { fill: #e1e1e1;font-weight: bold } +.terminal-r8 { fill: #e0e0e0;font-style: italic; } +.terminal-r9 { fill: #7ae998 } +.terminal-r10 { fill: #6db2ff } +.terminal-r11 { fill: #55c076;font-weight: bold } +.terminal-r12 { fill: #ddedf9;font-weight: bold } +.terminal-r13 { fill: #008139 } +.terminal-r14 { fill: #004295 } +.terminal-r15 { fill: #e1e1e1;text-decoration: underline; } +.terminal-r16 { fill: #ffa62b;font-weight: bold } +.terminal-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the ● Your pipeline will never be part of nf-core -nf-core community● You want full control over all features that -● You think that there's an outside chance are included from the template (including  -that it ever could be part of nf-corethose that are mandatory for nf-core). - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the● Your pipeline will never be part of nf-core +nf-core community● You want full control over all features that +● You think that there's an outside chanceare included from the template (including +that it ever could be part of nf-corethose that are mandatory for nf-core). + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 3549e5e09f..b8a712465f 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,258 +19,258 @@ font-weight: 700; } - .terminal-682353586-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-682353586-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-682353586-r1 { fill: #c5c8c6 } -.terminal-682353586-r2 { fill: #e0e0e0 } 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- + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. -▅▅ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of  Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: - -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -Continuous Integration & Testing - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. +▅▅ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +Continuous Integration & Testing + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index c04d611ef6..3e0fe54057 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,249 +19,249 @@ font-weight: 700; } - .terminal-3673759274-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3673759274-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3673759274-r1 { fill: #c5c8c6 } -.terminal-3673759274-r2 { fill: #e0e0e0 } -.terminal-3673759274-r3 { fill: #94999c } -.terminal-3673759274-r4 { fill: #0178d4;font-weight: bold } -.terminal-3673759274-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-3673759274-r6 { fill: #121212 } -.terminal-3673759274-r7 { fill: #008139 } -.terminal-3673759274-r8 { fill: #b93c5b } -.terminal-3673759274-r9 { fill: #2d2d2d } -.terminal-3673759274-r10 { fill: #7ae998 } -.terminal-3673759274-r11 { fill: #e0e0e0;font-weight: bold } -.terminal-3673759274-r12 { fill: #0a180e;font-weight: bold } -.terminal-3673759274-r13 { fill: #0d0d0d } -.terminal-3673759274-r14 { fill: #495259 } -.terminal-3673759274-r15 { fill: #ffa62b;font-weight: bold } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #008139 } +.terminal-r8 { fill: #b93c5b } +.terminal-r9 { fill: #2d2d2d } +.terminal-r10 { fill: #7ae998 } +.terminal-r11 { fill: #e0e0e0;font-weight: bold } +.terminal-r12 { fill: #0a180e;font-weight: bold } +.terminal-r13 { fill: #0d0d0d } +.terminal-r14 { fill: #495259 } +.terminal-r15 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Final details - - - - -First version of the pipelinePath to the output directory where the  -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Final details + + + + +First version of the pipelinePath to the output directory where the +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 823cc7827e..6c83c1497b 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-4250860474-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4250860474-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4250860474-r1 { fill: #c5c8c6 } -.terminal-4250860474-r2 { fill: #e0e0e0 } -.terminal-4250860474-r3 { fill: #94999c } -.terminal-4250860474-r4 { fill: #0178d4;font-weight: bold } -.terminal-4250860474-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-4250860474-r6 { fill: #2d2d2d } -.terminal-4250860474-r7 { fill: #e0e0e0;font-weight: 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fill: #2d2d2d } +.terminal-r7 { fill: #e0e0e0;font-weight: bold } +.terminal-r8 { fill: #121212 } +.terminal-r9 { fill: #008139 } +.terminal-r10 { fill: #0d0d0d } +.terminal-r11 { fill: #b93c5b } +.terminal-r12 { fill: #0f4b79 } +.terminal-r13 { fill: #a0a0a0;font-weight: bold } +.terminal-r14 { fill: #191919 } +.terminal-r15 { fill: #1e1e1e } +.terminal-r16 { fill: #808080 } +.terminal-r17 { fill: #7ae998 } +.terminal-r18 { fill: #6db2ff } +.terminal-r19 { fill: #0a180e;font-weight: bold } +.terminal-r20 { fill: #ddedf9;font-weight: bold } +.terminal-r21 { fill: #004295 } +.terminal-r22 { fill: #495259 } +.terminal-r23 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Create GitHub repository - -Now that we have created a new pipeline locally, we can create a new GitHub repository and push  -the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -The name of the organisation where the The name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user  -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + +Now that we have created a new pipeline locally, we can create a new GitHub repository and push +the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +The name of the organisation where theThe name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index 54a14534cb..f28631fc53 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,251 +19,252 @@ font-weight: 700; } - .terminal-167342788-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-167342788-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-167342788-r1 { fill: #c5c8c6 } -.terminal-167342788-r2 { fill: #e0e0e0 } -.terminal-167342788-r3 { fill: #94999c } -.terminal-167342788-r4 { fill: #0178d4;font-weight: bold } -.terminal-167342788-r5 { fill: #008000 } -.terminal-167342788-r6 { fill: #ffff00 } -.terminal-167342788-r7 { fill: #4ebf71;font-weight: bold } -.terminal-167342788-r8 { fill: #d2d2d2 } -.terminal-167342788-r9 { fill: #82aaff } -.terminal-167342788-r10 { fill: #eeffff } -.terminal-167342788-r11 { fill: #18954b } -.terminal-167342788-r12 { fill: #959595;font-weight: bold } -.terminal-167342788-r13 { fill: #7ae998 } -.terminal-167342788-r14 { fill: #55c076;font-weight: bold } -.terminal-167342788-r15 { fill: #008139 } -.terminal-167342788-r16 { fill: #ffa62b;font-weight: bold } -.terminal-167342788-r17 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #008000 } +.terminal-r6 { fill: #0000ff } +.terminal-r7 { fill: #ffff00 } +.terminal-r8 { fill: #e1e1e1;font-weight: bold } +.terminal-r9 { fill: #d2d2d2 } +.terminal-r10 { fill: #82aaff } +.terminal-r11 { fill: #eeffff } +.terminal-r12 { fill: #0f4b79 } +.terminal-r13 { fill: #a0a0a0;font-weight: bold } +.terminal-r14 { fill: #7ae998 } +.terminal-r15 { fill: #55c076;font-weight: bold } +.terminal-r16 { fill: #008139 } +.terminal-r17 { fill: #ffa62b;font-weight: bold } +.terminal-r18 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -If you would like to create the GitHub repository later, you can do it manually by following  -these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +If you would like to create the GitHub repository later, you can do it manually by following +these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 8847cc9021..77494c0bfe 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,246 +19,246 @@ font-weight: 700; } - .terminal-309664288-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-309664288-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-309664288-r1 { fill: #c5c8c6 } -.terminal-309664288-r2 { fill: #e0e0e0 } -.terminal-309664288-r3 { fill: #94999c } -.terminal-309664288-r4 { fill: #0178d4;font-weight: bold } -.terminal-309664288-r5 { fill: #7ae998 } -.terminal-309664288-r6 { fill: #6db2ff } -.terminal-309664288-r7 { fill: #55c076;font-weight: bold } -.terminal-309664288-r8 { fill: #ddedf9;font-weight: bold } -.terminal-309664288-r9 { fill: #008139 } -.terminal-309664288-r10 { fill: #004295 } -.terminal-309664288-r11 { fill: #ffa62b;font-weight: bold } -.terminal-309664288-r12 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #7ae998 } +.terminal-r6 { fill: #6db2ff } +.terminal-r7 { fill: #55c076;font-weight: bold } +.terminal-r8 { fill: #ddedf9;font-weight: bold } +.terminal-r9 { fill: #008139 } +.terminal-r10 { fill: #004295 } +.terminal-r11 { fill: #ffa62b;font-weight: bold } +.terminal-r12 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Create GitHub repository - - -After creating the pipeline template locally, we can create a GitHub repository and push the  -code to it. - -Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + + +After creating the pipeline template locally, we can create a GitHub repository and push the +code to it. + +Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 20f874c94f..a8c3c4ffd2 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-3243908447-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3243908447-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3243908447-r1 { fill: #c5c8c6 } -.terminal-3243908447-r2 { fill: #e0e0e0 } -.terminal-3243908447-r3 { fill: #94999c } -.terminal-3243908447-r4 { fill: #0178d4;font-weight: bold } -.terminal-3243908447-r5 { fill: #121212 } -.terminal-3243908447-r6 { fill: #0178d4 } -.terminal-3243908447-r7 { fill: #272727 } -.terminal-3243908447-r8 { fill: #191919 } -.terminal-3243908447-r9 { fill: #6db2ff } -.terminal-3243908447-r10 { 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+.terminal-r13 { fill: #004295 } +.terminal-r14 { fill: #2d2d2d } +.terminal-r15 { fill: #7ae998 } +.terminal-r16 { fill: #e0e0e0;font-weight: bold } +.terminal-r17 { fill: #0a180e;font-weight: bold } +.terminal-r18 { fill: #0d0d0d } +.terminal-r19 { fill: #008139 } +.terminal-r20 { fill: #ffa62b;font-weight: bold } +.terminal-r21 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub  Show help  -▊▁▁▁▁▁▁▁▁▎repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -Continuous Integration & Testing - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous  -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add testing profilesAdd two default testing  Show help  -▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add pipeline testingAdd pipeline testing  Show help  -▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add pipeline testingAdd pipeline testing Show help  +▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 6c960fdc3f..f594d2348a 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-201882774-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-201882774-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-201882774-r1 { fill: #c5c8c6 } -.terminal-201882774-r2 { fill: #e0e0e0 } -.terminal-201882774-r3 { fill: #94999c } -.terminal-201882774-r4 { fill: #0178d4;font-weight: bold } -.terminal-201882774-r5 { fill: #121212 } -.terminal-201882774-r6 { fill: #191919 } -.terminal-201882774-r7 { fill: #6db2ff } -.terminal-201882774-r8 { fill: #1e1e1e } -.terminal-201882774-r9 { fill: #808080 } -.terminal-201882774-r10 { fill: #ddedf9;font-weight: bold } -.terminal-201882774-r11 { fill: #004295 } -.terminal-201882774-r12 { fill: #2d2d2d } -.terminal-201882774-r13 { fill: #7ae998 } -.terminal-201882774-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-201882774-r15 { fill: #0a180e;font-weight: bold } -.terminal-201882774-r16 { fill: #0d0d0d } -.terminal-201882774-r17 { fill: #008139 } -.terminal-201882774-r18 { fill: #ffa62b;font-weight: bold } -.terminal-201882774-r19 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #121212 } +.terminal-r6 { fill: #191919 } +.terminal-r7 { fill: #6db2ff } +.terminal-r8 { fill: #1e1e1e } +.terminal-r9 { fill: #808080 } +.terminal-r10 { fill: #ddedf9;font-weight: bold } +.terminal-r11 { fill: #004295 } +.terminal-r12 { fill: #2d2d2d } +.terminal-r13 { fill: #7ae998 } +.terminal-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-r15 { fill: #0a180e;font-weight: bold } +.terminal-r16 { fill: #0d0d0d } +.terminal-r17 { fill: #008139 } +.terminal-r18 { fill: #ffa62b;font-weight: bold } +.terminal-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Template features - - -Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common  -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report  -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control  -analysis of input FASTQ  -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema  Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use GPUAdd GPU support to the  Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use reference genomesThe pipeline will be Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +of the most common +reference genome files +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use multiqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +generates an HTML report +for quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use fastqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +performs quality control +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use nf-schemaUse the nf-schema Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use GPUAdd GPU support to the Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 2f80eff0d5..4d3a837545 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-243002673-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-243002673-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-243002673-r1 { fill: #c5c8c6 } -.terminal-243002673-r2 { fill: #e0e0e0 } -.terminal-243002673-r3 { fill: #94999c } -.terminal-243002673-r4 { fill: #0178d4;font-weight: bold } -.terminal-243002673-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-243002673-r6 { fill: #121212 } -.terminal-243002673-r7 { fill: #084724 } -.terminal-243002673-r8 { fill: #762b3d } -.terminal-243002673-r9 { fill: #a2a2a2 } -.terminal-243002673-r10 { fill: #737373 } -.terminal-243002673-r11 { fill: #b93c5b } -.terminal-243002673-r12 { fill: #2d2d2d } -.terminal-243002673-r13 { fill: #7ae998 } -.terminal-243002673-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-243002673-r15 { fill: #55c076;font-weight: bold } -.terminal-243002673-r16 { fill: #0d0d0d } -.terminal-243002673-r17 { fill: #008139 } -.terminal-243002673-r18 { fill: #ffa62b;font-weight: bold } -.terminal-243002673-r19 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #084724 } +.terminal-r8 { fill: #762b3d } +.terminal-r9 { fill: #a2a2a2 } +.terminal-r10 { fill: #737373 } +.terminal-r11 { fill: #b93c5b } +.terminal-r12 { fill: #2d2d2d } +.terminal-r13 { fill: #7ae998 } +.terminal-r14 { fill: #e0e0e0;font-weight: bold } +.terminal-r15 { fill: #55c076;font-weight: bold } +.terminal-r16 { fill: #0d0d0d } +.terminal-r17 { fill: #008139 } +.terminal-r18 { fill: #ffa62b;font-weight: bold } +.terminal-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 59698b22ef..875d7139cd 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,249 +19,250 @@ font-weight: 700; } - .terminal-1605040715-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1605040715-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1605040715-r1 { fill: #c5c8c6 } -.terminal-1605040715-r2 { fill: #e0e0e0 } -.terminal-1605040715-r3 { fill: #94999c } -.terminal-1605040715-r4 { fill: #008000 } -.terminal-1605040715-r5 { fill: #ffff00 } -.terminal-1605040715-r6 { fill: #0178d4;font-weight: bold } -.terminal-1605040715-r7 { fill: #e1e1e1;text-decoration: underline; } -.terminal-1605040715-r8 { fill: #18954b } -.terminal-1605040715-r9 { fill: #e2e2e2;text-decoration: underline; } -.terminal-1605040715-r10 { fill: #e0e0e0;font-weight: bold;font-style: italic; } -.terminal-1605040715-r11 { fill: #7ae998 } -.terminal-1605040715-r12 { fill: #55c076;font-weight: bold } -.terminal-1605040715-r13 { fill: #008139 } -.terminal-1605040715-r14 { fill: #ffa62b;font-weight: bold } -.terminal-1605040715-r15 { fill: #495259 } + .terminal-r1 { fill: #c5c8c6 } +.terminal-r2 { fill: #e0e0e0 } +.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #008000 } +.terminal-r5 { fill: #0000ff } +.terminal-r6 { fill: #ffff00 } +.terminal-r7 { fill: #0178d4;font-weight: bold } +.terminal-r8 { fill: #e1e1e1;text-decoration: underline; } +.terminal-r9 { fill: #0f4b79 } +.terminal-r10 { fill: #e2e2e2;text-decoration: underline; } +.terminal-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } +.terminal-r12 { fill: #7ae998 } +.terminal-r13 { fill: #55c076;font-weight: bold } +.terminal-r14 { fill: #008139 } +.terminal-r15 { fill: #ffa62b;font-weight: bold } +.terminal-r16 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline  - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core  -pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the  -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all                                               ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core +pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette From 6135c45492435a7c330959e5c1f4ebba464c85b1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 09:20:29 +0000 Subject: [PATCH 22/33] fix test_customisation_help snapshot --- tests/pipelines/test_create_app.py | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/pipelines/test_create_app.py b/tests/pipelines/test_create_app.py index e359cc34e0..abc4d56ef9 100644 --- a/tests/pipelines/test_create_app.py +++ b/tests/pipelines/test_create_app.py @@ -182,6 +182,7 @@ async def run_before(pilot) -> None: await pilot.press("tab") await pilot.press("M", "e") await pilot.click("#next") + await pilot.press("^p") await pilot.click("#github_badges") await pilot.press("tab") await pilot.press("enter") From e3b1c728eb07ebd02370b450047d5f1dfc9acf65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Thu, 26 Jun 2025 09:49:05 +0000 Subject: [PATCH 23/33] fix toggle_all binding --- nf_core/pipelines/create/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index a4d457d623..8b873eaa6c 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -104,7 +104,7 @@ def action_toggle_dark(self) -> None: def action_toggle_all(self) -> None: """An action to toggle all Switches.""" - switches = self.query(Switch) + switches = self.screen.query("Switch") if not switches: return # No Switches widgets found # Determine the new state based on the first switch From a4457f912796e564074c60a8c171fac9b070d97c Mon Sep 17 00:00:00 2001 From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com> Date: Thu, 26 Jun 2025 14:22:06 +0200 Subject: [PATCH 24/33] Update nf_core/pipelines/create/create.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/create.py | 15 ++++++++------- 1 file changed, 8 insertions(+), 7 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 9ef431dfcb..54b3e70aa9 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -113,13 +113,14 @@ def __init__( # Get list of files we're skipping with the supplied skip keys - skip_paths: list = [] - for feature in self.skip_areas: - for section in self.template_features_yml.values(): - if feature in section["features"]: - if section["features"][feature]["skippable_paths"]: - skip_paths = skip_paths + section["features"][feature]["skippable_paths"] - self.skip_paths = set(skip_paths) +skip_paths = [ + path + for feature in self.skip_areas + for section in self.template_features_yml.values() + if feature in section["features"] and section["features"][feature]["skippable_paths"] + for path in section["features"][feature]["skippable_paths"] +] +self.skip_paths = set(skip_paths) # Set convenience variables self.name = self.config.name From 21dacd4339a531a369485416168205b163178611 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Thu, 26 Jun 2025 14:35:37 +0200 Subject: [PATCH 25/33] formatting --- nf_core/pipelines/create/create.py | 36 ++++++++++++++++-------------- 1 file changed, 19 insertions(+), 17 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 54b3e70aa9..0a6035def1 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -113,14 +113,14 @@ def __init__( # Get list of files we're skipping with the supplied skip keys -skip_paths = [ - path - for feature in self.skip_areas - for section in self.template_features_yml.values() - if feature in section["features"] and section["features"][feature]["skippable_paths"] - for path in section["features"][feature]["skippable_paths"] -] -self.skip_paths = set(skip_paths) + skip_paths = [ + path + for feature in self.skip_areas + for section in self.template_features_yml.values() + if feature in section["features"] and section["features"][feature]["skippable_paths"] + for path in section["features"][feature]["skippable_paths"] + ] + self.skip_paths = set(skip_paths) # Set convenience variables self.name = self.config.name @@ -221,15 +221,17 @@ def obtain_jinja_params_dict( jinja_params = self.config.model_dump(exclude_none=True) # Add template areas to jinja params and create list of areas with paths to skip - skip_areas = [] - for section in self.template_features_yml.values(): - for t_area in section["features"].keys(): - if t_area in features_to_skip: - if section["features"][t_area]["skippable_paths"]: - skip_areas.append(t_area) - jinja_params[t_area] = False - else: - jinja_params[t_area] = True + skip_areas = [ + t_area + for section in self.template_features_yml.values() + for t_area, feat in section["features"].items() + if t_area in features_to_skip and feat.get("skippable_paths") + ] + jinja_params = { + t_area: (t_area not in features_to_skip) + for section in self.template_features_yml.values() + for t_area in section["features"].keys() + } # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files if not self.config.is_nfcore: From 6cac3f276405f484545f44c0fd6f49f09b94e0b2 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Thu, 26 Jun 2025 15:23:58 +0200 Subject: [PATCH 26/33] debug --- nf_core/pipelines/create/create.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 0a6035def1..a2ff518d13 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -224,8 +224,9 @@ def obtain_jinja_params_dict( skip_areas = [ t_area for section in self.template_features_yml.values() - for t_area, feat in section["features"].items() - if t_area in features_to_skip and feat.get("skippable_paths") + for t_area in section["features"].keys() + if t_area in features_to_skip and section["features"][t_area]["skippable_paths"] + # for t_area in section["features"][t_area]["skippable_paths"] ] jinja_params = { t_area: (t_area not in features_to_skip) From a6232f2c978d21fea3e0ab872381e3b3778427f5 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Thu, 26 Jun 2025 15:33:36 +0200 Subject: [PATCH 27/33] debug --- nf_core/pipelines/create/create.py | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index a2ff518d13..c144586073 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -228,11 +228,13 @@ def obtain_jinja_params_dict( if t_area in features_to_skip and section["features"][t_area]["skippable_paths"] # for t_area in section["features"][t_area]["skippable_paths"] ] - jinja_params = { - t_area: (t_area not in features_to_skip) - for section in self.template_features_yml.values() - for t_area in section["features"].keys() - } + jinja_params.update( + { + t_area: t_area not in features_to_skip + for section in self.template_features_yml.values() + for t_area in section["features"] + } + ) # Add is_nfcore as an area to skip for non-nf-core pipelines, to skip all nf-core files if not self.config.is_nfcore: From a4a138118a5fc13cf700b1bf10fdb96503615d48 Mon Sep 17 00:00:00 2001 From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com> Date: Thu, 26 Jun 2025 15:44:58 +0200 Subject: [PATCH 28/33] Update nf_core/pipelines/create/custompipeline.py MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Matthias Hörtenhuber --- nf_core/pipelines/create/custompipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 0d45feedb7..1df2976d2c 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -37,7 +37,7 @@ def compose(self) -> ComposeResult: def on_mount(self) -> None: for section_name, section in self.parent.template_features_yml.items(): - section_title = section["name"] + section_title = "## " +section["name"] features = section["features"] show_section = False self.query_one("#features").mount( From 7560674e4b3eb683c892ed94cd086d7040867c32 Mon Sep 17 00:00:00 2001 From: yuxinNing Date: Thu, 26 Jun 2025 15:53:39 +0200 Subject: [PATCH 29/33] pre-commit --- nf_core/pipelines/create/custompipeline.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 1df2976d2c..357cff8762 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -37,7 +37,7 @@ def compose(self) -> ComposeResult: def on_mount(self) -> None: for section_name, section in self.parent.template_features_yml.items(): - section_title = "## " +section["name"] + section_title = "## " + section["name"] features = section["features"] show_section = False self.query_one("#features").mount( From 3f0c0616eb633c870435b4028c1285da0b572a9b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 26 Jun 2025 14:23:57 +0000 Subject: [PATCH 30/33] [automated] Update Textual snapshots --- .../test_customisation_help.svg | 107 +++---- .../test_create_app/test_github_details.svg | 275 ------------------ .../test_github_exit_message.svg | 270 ----------------- .../test_create_app/test_github_question.svg | 220 +------------- .../test_create_app/test_type_custom.svg | 104 +++---- 5 files changed, 114 insertions(+), 862 deletions(-) delete mode 100644 tests/pipelines/__snapshots__/test_create_app/test_github_details.svg delete mode 100644 tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index b8a712465f..0adf318a71 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -39,23 +39,24 @@ .terminal-r5 { fill: #121212 } .terminal-r6 { fill: #191919 } .terminal-r7 { fill: #1e1e1e } -.terminal-r8 { fill: #6db2ff } -.terminal-r9 { fill: #808080 } -.terminal-r10 { fill: #ddedf9;font-weight: bold } -.terminal-r11 { fill: #004295 } +.terminal-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-r9 { fill: #6db2ff } +.terminal-r10 { fill: #808080 } +.terminal-r11 { fill: #ddedf9;font-weight: bold } .terminal-r12 { fill: #000000 } -.terminal-r13 { fill: #0178d4 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #272727 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0d0d0d } -.terminal-r18 { fill: #a5a5a5;font-weight: bold } -.terminal-r19 { fill: #e4e4e4;font-weight: bold } -.terminal-r20 { fill: #7ae998 } -.terminal-r21 { fill: #0a180e;font-weight: bold } -.terminal-r22 { fill: #008139 } -.terminal-r23 { fill: #ffa62b;font-weight: bold } -.terminal-r24 { fill: #495259 } +.terminal-r13 { fill: #004295 } +.terminal-r14 { fill: #0178d4 } +.terminal-r15 { fill: #2d2d2d } +.terminal-r16 { fill: #272727 } +.terminal-r17 { fill: #e0e0e0;font-weight: bold } +.terminal-r18 { fill: #0d0d0d } +.terminal-r19 { fill: #a5a5a5;font-weight: bold } +.terminal-r20 { fill: #e4e4e4;font-weight: bold } +.terminal-r21 { fill: #7ae998 } +.terminal-r22 { fill: #0a180e;font-weight: bold } +.terminal-r23 { fill: #008139 } +.terminal-r24 { fill: #ffa62b;font-weight: bold } +.terminal-r25 { fill: #495259 } @@ -219,7 +220,7 @@ - + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline @@ -230,47 +231,47 @@ ▊▔▔▔▔▔▔▔▔▎ ▊▎Toggle all features ▊▁▁▁▁▁▁▁▁▎ -Repository Setup + - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. -▅▅ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg deleted file mode 100644 index 6c83c1497b..0000000000 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ /dev/null @@ -1,275 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core pipelines create - - - - - - - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - -Now that we have created a new pipeline locally, we can create a new GitHub repository and push -the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊GitHub username▎▊••••••••••••                  ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -The name of the organisation where theThe name of the new GitHub repository -GitHub repo will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                               ▎▊mypipeline                            ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -▌⚠️ You can't create a repository directly in the nf-core organisation. -▌Please create the pipeline repo to an organisation where you have access or use your user -▌account. A core-team member will be able to transfer the repo to nf-core once the development -▌has started. - -▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▊▔▔▔▔▔▔▔▔▎Private -▊▎Select to make the new GitHub repo private. -▊▁▁▁▁▁▁▁▁▎ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - -▏^p palette - - - diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg deleted file mode 100644 index f28631fc53..0000000000 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ /dev/null @@ -1,270 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - nf-core pipelines create - - - - - - - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -If you would like to create the GitHub repository later, you can do it manually by following -these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -▌💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette - - - diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 77494c0bfe..3804c6b773 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -1,4 +1,4 @@ - + - + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + - nf-core pipelines create + nf-core pipelines create @@ -207,58 +50,9 @@ - + - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Create GitHub repository - - -After creating the pipeline template locally, we can create a GitHub repository and push the -code to it. - -Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index a8c3c4ffd2..df8d2ee879 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -39,20 +39,22 @@ .terminal-r5 { fill: #121212 } .terminal-r6 { fill: #0178d4 } .terminal-r7 { fill: #272727 } -.terminal-r8 { fill: #191919 } -.terminal-r9 { fill: #6db2ff } -.terminal-r10 { fill: #1e1e1e } -.terminal-r11 { fill: #808080 } -.terminal-r12 { fill: #ddedf9;font-weight: bold } -.terminal-r13 { fill: #004295 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #7ae998 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0a180e;font-weight: bold } -.terminal-r18 { fill: #0d0d0d } -.terminal-r19 { fill: #008139 } -.terminal-r20 { fill: #ffa62b;font-weight: bold } -.terminal-r21 { fill: #495259 } +.terminal-r8 { fill: #0178d4;text-decoration: underline; } +.terminal-r9 { fill: #191919 } +.terminal-r10 { fill: #6db2ff } +.terminal-r11 { fill: #1e1e1e } +.terminal-r12 { fill: #808080 } +.terminal-r13 { fill: #ddedf9;font-weight: bold } +.terminal-r14 { fill: #004295 } +.terminal-r15 { fill: #000000 } +.terminal-r16 { fill: #2d2d2d } +.terminal-r17 { fill: #7ae998 } +.terminal-r18 { fill: #e0e0e0;font-weight: bold } +.terminal-r19 { fill: #0a180e;font-weight: bold } +.terminal-r20 { fill: #0d0d0d } +.terminal-r21 { fill: #008139 } +.terminal-r22 { fill: #ffa62b;font-weight: bold } +.terminal-r23 { fill: #495259 } @@ -216,7 +218,7 @@ - + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline @@ -227,47 +229,47 @@ ▊▔▔▔▔▔▔▔▔▎ ▊▎Toggle all features ▊▁▁▁▁▁▁▁▁▎ -Repository Setup + - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -Continuous Integration & Testing +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add testing profilesAdd two default testing Show help  -▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) testing -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add pipeline testingAdd pipeline testing Show help  -▊▁▁▁▁▁▁▁▁▎using nf-test▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + d Toggle dark mode  q Quit  a Toggle all ▏^p palette From df1ce2d8cc3a41c4d014920c0f1d02409b68bf56 Mon Sep 17 00:00:00 2001 From: yuxin ning Date: Fri, 27 Jun 2025 13:23:53 +0000 Subject: [PATCH 31/33] snapshotupdate --- .../test_basic_details_custom.svg | 248 +++++++++-------- .../test_basic_details_nfcore.svg | 255 ++++++++--------- .../test_create_app/test_choose_type.svg | 246 ++++++++-------- .../test_customisation_help.svg | 262 +++++++++--------- .../test_create_app/test_final_details.svg | 245 ++++++++-------- .../test_create_app/test_type_custom.svg | 258 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 249 +++++++++-------- .../test_type_nfcore_validation.svg | 252 ++++++++--------- .../test_create_app/test_welcome.svg | 247 +++++++++-------- 9 files changed, 1136 insertions(+), 1126 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 3d74d0761e..f327dac799 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,251 +19,253 @@ font-weight: 700; } - .terminal-matrix { + .terminal-1837969819-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-1837969819-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #191919 } -.terminal-r9 { fill: #737373 } -.terminal-r10 { fill: #b93c5b } -.terminal-r11 { fill: #2d2d2d } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #e0e0e0;font-weight: bold } -.terminal-r14 { fill: #0a180e;font-weight: bold } -.terminal-r15 { fill: #0d0d0d } -.terminal-r16 { fill: #495259 } -.terminal-r17 { fill: #ffa62b;font-weight: bold } + .terminal-1837969819-r1 { fill: #c5c8c6 } +.terminal-1837969819-r2 { fill: #e3e3e3 } +.terminal-1837969819-r3 { fill: #989898 } +.terminal-1837969819-r4 { fill: #e1e1e1 } +.terminal-1837969819-r5 { fill: #4ebf71;font-weight: bold } +.terminal-1837969819-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-1837969819-r7 { fill: #1e1e1e } +.terminal-1837969819-r8 { fill: #008139 } +.terminal-1837969819-r9 { fill: #121212 } +.terminal-1837969819-r10 { fill: #e2e2e2 } +.terminal-1837969819-r11 { fill: #787878 } +.terminal-1837969819-r12 { fill: #454a50 } +.terminal-1837969819-r13 { fill: #7ae998 } +.terminal-1837969819-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-1837969819-r15 { fill: #0a180e;font-weight: bold } +.terminal-1837969819-r16 { fill: #000000 } +.terminal-1837969819-r17 { fill: #fea62b;font-weight: bold } +.terminal-1837969819-r18 { fill: #a7a9ab } +.terminal-1837969819-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 8ccef7d421..6a4e424130 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,255 +19,256 @@ font-weight: 700; } - .terminal-matrix { + .terminal-2735207764-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-2735207764-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #084724 } -.terminal-r8 { fill: #0178d4 } -.terminal-r9 { fill: #a2a2a2 } -.terminal-r10 { fill: #797979 } -.terminal-r11 { fill: #b93c5b } -.terminal-r12 { fill: #191919 } -.terminal-r13 { fill: #737373 } -.terminal-r14 { fill: #2d2d2d } -.terminal-r15 { fill: #7ae998 } -.terminal-r16 { fill: #e0e0e0;font-weight: bold } -.terminal-r17 { fill: #0a180e;font-weight: bold } -.terminal-r18 { fill: #0d0d0d } -.terminal-r19 { fill: #008139 } -.terminal-r20 { fill: #495259 } -.terminal-r21 { fill: #ffa62b;font-weight: bold } + .terminal-2735207764-r1 { fill: #c5c8c6 } +.terminal-2735207764-r2 { fill: #e3e3e3 } +.terminal-2735207764-r3 { fill: #989898 } +.terminal-2735207764-r4 { fill: #e1e1e1 } +.terminal-2735207764-r5 { fill: #4ebf71;font-weight: bold } +.terminal-2735207764-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-2735207764-r7 { fill: #1e1e1e } +.terminal-2735207764-r8 { fill: #0f4e2a } +.terminal-2735207764-r9 { fill: #0178d4 } +.terminal-2735207764-r10 { fill: #a7a7a7 } +.terminal-2735207764-r11 { fill: #787878 } +.terminal-2735207764-r12 { fill: #e2e2e2 } +.terminal-2735207764-r13 { fill: #121212 } +.terminal-2735207764-r14 { fill: #454a50 } +.terminal-2735207764-r15 { fill: #7ae998 } +.terminal-2735207764-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-2735207764-r17 { fill: #0a180e;font-weight: bold } +.terminal-2735207764-r18 { fill: #000000 } +.terminal-2735207764-r19 { fill: #008139 } +.terminal-2735207764-r20 { fill: #fea62b;font-weight: bold } +.terminal-2735207764-r21 { fill: #a7a9ab } +.terminal-2735207764-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 8c7c257684..3eaceeb477 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-matrix { + .terminal-2526112365-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-2526112365-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #0178d4;text-decoration: underline; } -.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } -.terminal-r7 { fill: #e1e1e1;font-weight: bold } -.terminal-r8 { fill: #e0e0e0;font-style: italic; } -.terminal-r9 { fill: #7ae998 } -.terminal-r10 { fill: #6db2ff } -.terminal-r11 { fill: #55c076;font-weight: bold } -.terminal-r12 { fill: #ddedf9;font-weight: bold } -.terminal-r13 { fill: #008139 } -.terminal-r14 { fill: #004295 } -.terminal-r15 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r16 { fill: 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the● Your pipeline will never be part of nf-core -nf-core community● You want full control over all features that -● You think that there's an outside chanceare included from the template (including -that it ever could be part of nf-corethose that are mandatory for nf-core). - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the ● Your pipeline will never be part of  +nf-core communitynf-core +● You think that there's an outside chance ● You want full control over all features  +that it ever could be part of nf-corethat are included from the template  +(including those that are mandatory for  +nf-core). +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +  Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 0adf318a71..921ede58b0 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,259 +19,259 @@ font-weight: 700; } - .terminal-matrix { + .terminal-4282614070-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; 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+.terminal-4282614070-r19 { fill: #9d9d9d;font-weight: bold } +.terminal-4282614070-r20 { fill: #7ae998 } +.terminal-4282614070-r21 { fill: #0a180e;font-weight: bold } +.terminal-4282614070-r22 { fill: #008139 } +.terminal-4282614070-r23 { fill: #fea62b;font-weight: bold } +.terminal-4282614070-r24 { fill: #a7a9ab } +.terminal-4282614070-r25 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: - -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎        Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help ▅▅ +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a changelogAdd a CHANGELOG.md  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index 3e0fe54057..c54e2211f8 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,249 +19,252 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3263959949-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3263959949-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #a0a0a0;font-style: italic; } -.terminal-r6 { fill: #121212 } -.terminal-r7 { fill: #008139 } -.terminal-r8 { fill: #b93c5b } -.terminal-r9 { fill: #2d2d2d } -.terminal-r10 { fill: #7ae998 } -.terminal-r11 { fill: #e0e0e0;font-weight: bold } -.terminal-r12 { fill: #0a180e;font-weight: bold } -.terminal-r13 { fill: #0d0d0d } -.terminal-r14 { fill: #495259 } -.terminal-r15 { fill: #ffa62b;font-weight: bold } + .terminal-3263959949-r1 { fill: #c5c8c6 } +.terminal-3263959949-r2 { fill: #e3e3e3 } +.terminal-3263959949-r3 { fill: #989898 } +.terminal-3263959949-r4 { fill: #e1e1e1 } +.terminal-3263959949-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3263959949-r6 { fill: #1e1e1e } +.terminal-3263959949-r7 { fill: #507bb3 } +.terminal-3263959949-r8 { fill: #e2e2e2 } +.terminal-3263959949-r9 { fill: #808080 } +.terminal-3263959949-r10 { fill: #dde6ed;font-weight: bold } +.terminal-3263959949-r11 { fill: #001541 } +.terminal-3263959949-r12 { fill: #454a50 } +.terminal-3263959949-r13 { fill: #166d39 } +.terminal-3263959949-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-3263959949-r15 { fill: #3c8b54;font-weight: bold } +.terminal-3263959949-r16 { fill: #000000 } +.terminal-3263959949-r17 { fill: #5aa86f } +.terminal-3263959949-r18 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Final details - - - - -First version of the pipelinePath to the output directory where the -pipeline will be created -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊1.0.0dev▎▊.                                         ▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +  Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use multiqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use fastqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + +  Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use GPUAdd GPU support to the  Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index df8d2ee879..1fc4daf0b4 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3335347483-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3335347483-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #0178d4 } -.terminal-r7 { fill: #272727 } -.terminal-r8 { fill: #0178d4;text-decoration: underline; } -.terminal-r9 { fill: #191919 } -.terminal-r10 { fill: #6db2ff } -.terminal-r11 { fill: #1e1e1e } -.terminal-r12 { fill: #808080 } -.terminal-r13 { fill: #ddedf9;font-weight: bold } -.terminal-r14 { fill: #004295 } -.terminal-r15 { fill: #000000 } -.terminal-r16 { fill: #2d2d2d } -.terminal-r17 { fill: #7ae998 } -.terminal-r18 { fill: #e0e0e0;font-weight: bold } -.terminal-r19 { fill: #0a180e;font-weight: bold } -.terminal-r20 { fill: #0d0d0d } -.terminal-r21 { fill: #008139 } -.terminal-r22 { fill: #ffa62b;font-weight: bold } -.terminal-r23 { fill: #495259 } + .terminal-3335347483-r1 { fill: #c5c8c6 } +.terminal-3335347483-r2 { fill: #e3e3e3 } +.terminal-3335347483-r3 { fill: #989898 } +.terminal-3335347483-r4 { fill: #e1e1e1 } +.terminal-3335347483-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3335347483-r6 { fill: #1e1e1e } +.terminal-3335347483-r7 { fill: #0178d4 } +.terminal-3335347483-r8 { fill: #e2e2e2 } +.terminal-3335347483-r9 { fill: #4ebf71;text-decoration: underline; } +.terminal-3335347483-r10 { fill: #507bb3 } +.terminal-3335347483-r11 { fill: #808080 } +.terminal-3335347483-r12 { fill: #dde6ed;font-weight: bold } +.terminal-3335347483-r13 { fill: #14191f } +.terminal-3335347483-r14 { fill: #001541 } +.terminal-3335347483-r15 { fill: #454a50 } +.terminal-3335347483-r16 { fill: #7ae998 } +.terminal-3335347483-r17 { fill: #e2e3e3;font-weight: bold } +.terminal-3335347483-r18 { fill: #0a180e;font-weight: bold } +.terminal-3335347483-r19 { fill: #000000 } +.terminal-3335347483-r20 { fill: #008139 } +.terminal-3335347483-r21 { fill: #fea62b;font-weight: bold } +.terminal-3335347483-r22 { fill: #a7a9ab } +.terminal-3335347483-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use a GitHub repository.Create a GitHub Show help  -▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github badgesThe README.md file of Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a changelogAdd a CHANGELOG.md file. Show help  -▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add a license FileAdd the MIT license Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Continuous Integration & Testing - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add Github CI testsThe pipeline will Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI) testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Add testing profilesAdd two default testing Show help  -▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎        Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use a GitHub Create a GitHub  Show help ▁▁ +▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github badgesThe README.md file of  Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a changelogAdd a CHANGELOG.md  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add a license FileAdd the MIT license  Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Add Github CI testsThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index f594d2348a..6376b27a83 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,253 +19,252 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3705475042-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3705475042-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: #121212 } -.terminal-r6 { fill: #191919 } -.terminal-r7 { fill: #6db2ff } -.terminal-r8 { fill: #1e1e1e } -.terminal-r9 { fill: #808080 } -.terminal-r10 { fill: #ddedf9;font-weight: bold } -.terminal-r11 { fill: #004295 } -.terminal-r12 { fill: #2d2d2d } -.terminal-r13 { fill: #7ae998 } -.terminal-r14 { fill: #e0e0e0;font-weight: bold } -.terminal-r15 { fill: #0a180e;font-weight: bold } -.terminal-r16 { fill: #0d0d0d } -.terminal-r17 { fill: #008139 } -.terminal-r18 { fill: #ffa62b;font-weight: bold } -.terminal-r19 { fill: #495259 } + .terminal-3705475042-r1 { fill: #c5c8c6 } +.terminal-3705475042-r2 { fill: #e3e3e3 } +.terminal-3705475042-r3 { fill: #989898 } +.terminal-3705475042-r4 { fill: #e1e1e1 } +.terminal-3705475042-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3705475042-r6 { fill: #1e1e1e } +.terminal-3705475042-r7 { fill: #507bb3 } +.terminal-3705475042-r8 { fill: #e2e2e2 } +.terminal-3705475042-r9 { fill: #808080 } +.terminal-3705475042-r10 { fill: #dde6ed;font-weight: bold } +.terminal-3705475042-r11 { fill: #001541 } +.terminal-3705475042-r12 { fill: #454a50 } +.terminal-3705475042-r13 { fill: #7ae998 } +.terminal-3705475042-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-3705475042-r15 { fill: #0a180e;font-weight: bold } +.terminal-3705475042-r16 { fill: #000000 } +.terminal-3705475042-r17 { fill: #008139 } +.terminal-3705475042-r18 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Template features - - -Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use reference genomesThe pipeline will be Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -of the most common -reference genome files -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use multiqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -generates an HTML report -for quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use fastqcThe pipeline will include Show help  -▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -performs quality control -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use nf-schemaUse the nf-schema Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎Use GPUAdd GPU support to the Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +  Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use reference genomesThe pipeline will be  Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use multiqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use fastqcThe pipeline will  Show help  +▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use nf-schemaUse the nf-schema  Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + +  Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎        Use GPUAdd GPU support to the  Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 4d3a837545..fd6f2532c8 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,253 +19,255 @@ font-weight: 700; } - .terminal-matrix { + .terminal-3655041559-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-3655041559-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #0178d4;font-weight: bold } -.terminal-r5 { fill: 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fill: #a7a7a7 } +.terminal-3655041559-r11 { fill: #787878 } +.terminal-3655041559-r12 { fill: #e2e2e2 } +.terminal-3655041559-r13 { fill: #b93c5b } +.terminal-3655041559-r14 { fill: #454a50 } +.terminal-3655041559-r15 { fill: #7ae998 } +.terminal-3655041559-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3655041559-r17 { fill: #000000 } +.terminal-3655041559-r18 { fill: #008139 } +.terminal-3655041559-r19 { fill: #fea62b;font-weight: bold } +.terminal-3655041559-r20 { fill: #a7a9ab } +.terminal-3655041559-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index 875d7139cd..d9941b650d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,250 +19,253 @@ font-weight: 700; } - .terminal-matrix { + .terminal-2299823026-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-title { + .terminal-2299823026-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-r1 { fill: #c5c8c6 } -.terminal-r2 { fill: #e0e0e0 } -.terminal-r3 { fill: #a0a3a6 } -.terminal-r4 { fill: #008000 } -.terminal-r5 { fill: #0000ff } -.terminal-r6 { fill: #ffff00 } -.terminal-r7 { fill: #0178d4;font-weight: bold } -.terminal-r8 { fill: #e1e1e1;text-decoration: underline; } -.terminal-r9 { fill: #0f4b79 } -.terminal-r10 { fill: #e2e2e2;text-decoration: underline; } -.terminal-r11 { fill: #e0e0e0;font-weight: bold;font-style: italic; } -.terminal-r12 { fill: #7ae998 } -.terminal-r13 { fill: #55c076;font-weight: bold } -.terminal-r14 { fill: #008139 } -.terminal-r15 { fill: #ffa62b;font-weight: bold } -.terminal-r16 { fill: #495259 } + .terminal-2299823026-r1 { fill: #c5c8c6 } +.terminal-2299823026-r2 { fill: #e3e3e3 } +.terminal-2299823026-r3 { fill: #989898 } +.terminal-2299823026-r4 { fill: #98e024 } +.terminal-2299823026-r5 { fill: #626262 } +.terminal-2299823026-r6 { fill: #9d65ff } +.terminal-2299823026-r7 { fill: #fd971f } +.terminal-2299823026-r8 { fill: #e1e1e1 } +.terminal-2299823026-r9 { fill: #4ebf71;font-weight: bold } +.terminal-2299823026-r10 { fill: #e1e1e1;text-decoration: underline; } +.terminal-2299823026-r11 { fill: #18954b } +.terminal-2299823026-r12 { fill: #e2e2e2 } +.terminal-2299823026-r13 { fill: #e2e2e2;text-decoration: underline; } +.terminal-2299823026-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } +.terminal-2299823026-r15 { fill: #7ae998 } +.terminal-2299823026-r16 { fill: #008139 } +.terminal-2299823026-r17 { fill: #fea62b;font-weight: bold } +.terminal-2299823026-r18 { fill: #a7a9ab } +.terminal-2299823026-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core -pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    +  pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the  +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  From bfafb499c30a426e655d93a1a8b6a15699c58919 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 27 Jun 2025 13:38:53 +0000 Subject: [PATCH 32/33] [automated] Update Textual snapshots --- .../test_basic_details_custom.svg | 248 ++++++++--------- .../test_basic_details_nfcore.svg | 255 +++++++++-------- .../test_create_app/test_choose_type.svg | 246 ++++++++-------- .../test_customisation_help.svg | 262 +++++++++--------- .../test_create_app/test_final_details.svg | 245 ++++++++-------- .../test_create_app/test_type_custom.svg | 258 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 249 ++++++++--------- .../test_type_nfcore_validation.svg | 252 +++++++++-------- .../test_create_app/test_welcome.svg | 247 ++++++++--------- 9 files changed, 1126 insertions(+), 1136 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index f327dac799..3d74d0761e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,253 +19,251 @@ font-weight: 700; } - .terminal-1837969819-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1837969819-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1837969819-r1 { fill: #c5c8c6 } -.terminal-1837969819-r2 { fill: #e3e3e3 } -.terminal-1837969819-r3 { fill: #989898 } -.terminal-1837969819-r4 { fill: #e1e1e1 } -.terminal-1837969819-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1837969819-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-1837969819-r7 { fill: #1e1e1e } -.terminal-1837969819-r8 { fill: #008139 } -.terminal-1837969819-r9 { fill: #121212 } -.terminal-1837969819-r10 { fill: #e2e2e2 } -.terminal-1837969819-r11 { fill: #787878 } -.terminal-1837969819-r12 { fill: #454a50 } -.terminal-1837969819-r13 { fill: #7ae998 } 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 6a4e424130..8ccef7d421 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,256 +19,255 @@ font-weight: 700; } - .terminal-2735207764-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2735207764-title { + .terminal-title { font-size: 18px; font-weight: bold; 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- + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 3eaceeb477..8c7c257684 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - .terminal-2526112365-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2526112365-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - 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fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #0178d4;text-decoration: underline; } +.terminal-r6 { fill: #0178d4;font-style: italic;;text-decoration: underline; } +.terminal-r7 { fill: #e1e1e1;font-weight: bold } +.terminal-r8 { fill: #e0e0e0;font-style: italic; } +.terminal-r9 { fill: #7ae998 } +.terminal-r10 { fill: #6db2ff } +.terminal-r11 { fill: #55c076;font-weight: bold } +.terminal-r12 { fill: #ddedf9;font-weight: bold } +.terminal-r13 { fill: #008139 } +.terminal-r14 { fill: #004295 } +.terminal-r15 { fill: #e1e1e1;text-decoration: underline; } +.terminal-r16 { fill: #ffa62b;font-weight: bold } +.terminal-r17 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the ● Your pipeline will never be part of  -nf-core communitynf-core -● You think that there's an outside chance ● You want full control over all features  -that it ever could be part of nf-corethat are included from the template  -(including those that are mandatory for  -nf-core). -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -  Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the● Your pipeline will never be part of nf-core +nf-core community● You want full control over all features that +● You think that there's an outside chanceare included from the template (including +that it ever could be part of nf-corethose that are mandatory for nf-core). + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index 921ede58b0..0adf318a71 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,259 +19,259 @@ font-weight: 700; } - .terminal-4282614070-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-4282614070-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-4282614070-r1 { fill: #c5c8c6 } -.terminal-4282614070-r2 { fill: #e3e3e3 } -.terminal-4282614070-r3 { fill: #989898 } -.terminal-4282614070-r4 { fill: #e1e1e1 } 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+.terminal-r25 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎        Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use a GitHub Create a GitHub  Show help ▅▅ -▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github badgesThe README.md file of  Hide help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - - -The pipeline README.md will include badges for: - -● AWS CI Tests -● Zenodo DOI -● Nextflow -● nf-core template version -● Conda -● Docker -● Singularity -● Launching on Nextflow Tower - - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add a changelogAdd a CHANGELOG.md  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add a license FileAdd the MIT license  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help ▂▂ +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Hide help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + + +The pipeline README.md will include badges for: + +● AWS CI Tests +● Zenodo DOI +● Nextflow +● nf-core template version +● Conda +● Docker +● Singularity +● Launching on Nextflow Tower + + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index c54e2211f8..3e0fe54057 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,252 +19,249 @@ font-weight: 700; } - .terminal-3263959949-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3263959949-title { + 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+.terminal-r3 { fill: #a0a3a6 } +.terminal-r4 { fill: #0178d4;font-weight: bold } +.terminal-r5 { fill: #a0a0a0;font-style: italic; } +.terminal-r6 { fill: #121212 } +.terminal-r7 { fill: #008139 } +.terminal-r8 { fill: #b93c5b } +.terminal-r9 { fill: #2d2d2d } +.terminal-r10 { fill: #7ae998 } +.terminal-r11 { fill: #e0e0e0;font-weight: bold } +.terminal-r12 { fill: #0a180e;font-weight: bold } +.terminal-r13 { fill: #0d0d0d } +.terminal-r14 { fill: #495259 } +.terminal-r15 { fill: #ffa62b;font-weight: bold } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -  Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most common -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use multiqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which generates  -an HTML report for  -quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use fastqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which performs  -quality control  -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use nf-schemaUse the nf-schema  Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -this pipeline. - -  Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use GPUAdd GPU support to the  Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Final details + + + + +First version of the pipelinePath to the output directory where the +pipeline will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊1.0.0dev▎▊.                                         ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 1fc4daf0b4..df8d2ee879 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,257 +19,257 @@ font-weight: 700; } - 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+.terminal-r17 { fill: #7ae998 } +.terminal-r18 { fill: #e0e0e0;font-weight: bold } +.terminal-r19 { fill: #0a180e;font-weight: bold } +.terminal-r20 { fill: #0d0d0d } +.terminal-r21 { fill: #008139 } +.terminal-r22 { fill: #ffa62b;font-weight: bold } +.terminal-r23 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▊▔▔▔▔▔▔▔▔▎ -▊▎        Toggle all features -▊▁▁▁▁▁▁▁▁▎ - - -Repository Setup - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use a GitHub Create a GitHub  Show help ▁▁ -▊▁▁▁▁▁▁▁▁▎        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github badgesThe README.md file of  Show help  -▊▁▁▁▁▁▁▁▁▎the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add a changelogAdd a CHANGELOG.md  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add a license FileAdd the MIT license  Show help  -▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Continuous Integration & Testing - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Add Github CI testsThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +▊▔▔▔▔▔▔▔▔▎ +▊▎Toggle all features +▊▁▁▁▁▁▁▁▁▎ + + +Repository Setup + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use a GitHub repository.Create a GitHub Show help  +▊▁▁▁▁▁▁▁▁▎repository for the▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▆▆ +pipeline. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github badgesThe README.md file of Show help  +▊▁▁▁▁▁▁▁▁▎the pipeline will▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a changelogAdd a CHANGELOG.md file. Show help  +▊▁▁▁▁▁▁▁▁▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add a license FileAdd the MIT license Show help  +▊▁▁▁▁▁▁▁▁▎file.▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Continuous Integration & Testing + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add Github CI testsThe pipeline will Show help  +▊▁▁▁▁▁▁▁▁▎include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) testing + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Add testing profilesAdd two default testing Show help  +▊▁▁▁▁▁▁▁▁▎profiles▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index 6376b27a83..f594d2348a 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,252 +19,253 @@ font-weight: 700; } - .terminal-3705475042-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3705475042-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3705475042-r1 { fill: #c5c8c6 } -.terminal-3705475042-r2 { fill: #e3e3e3 } -.terminal-3705475042-r3 { fill: #989898 } -.terminal-3705475042-r4 { fill: #e1e1e1 } -.terminal-3705475042-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3705475042-r6 { fill: #1e1e1e } -.terminal-3705475042-r7 { fill: #507bb3 } -.terminal-3705475042-r8 { fill: #e2e2e2 } 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+.terminal-r15 { fill: #0a180e;font-weight: bold } +.terminal-r16 { fill: #0d0d0d } +.terminal-r17 { fill: #008139 } +.terminal-r18 { fill: #ffa62b;font-weight: bold } +.terminal-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -  Components & Modules - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use reference genomesThe pipeline will be  Show help  -▊▁▁▁▁▁▁▁▁▎configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most common -reference genome files  -from iGenomes - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use multiqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which generates  -an HTML report for  -quality control. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use fastqcThe pipeline will  Show help  -▊▁▁▁▁▁▁▁▁▎include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which performs  -quality control  -analysis of input FASTQ -files. - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use nf-schemaUse the nf-schema  Show help  -▊▁▁▁▁▁▁▁▁▎Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -this pipeline. - -  Configurations - - -▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -▊▎        Use GPUAdd GPU support to the  Show help  -▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Template features + + +Components & Modules + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use reference genomesThe pipeline will be Show help  +▊▁▁▁▁▁▁▁▁▎configured to use a copy▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +of the most common +reference genome files +from iGenomes + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use multiqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the MultiQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +generates an HTML report +for quality control. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use fastqcThe pipeline will include Show help  +▊▁▁▁▁▁▁▁▁▎the FastQC module which▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +performs quality control +analysis of input FASTQ +files. + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use nf-schemaUse the nf-schema Show help  +▊▁▁▁▁▁▁▁▁▎Nextflow plugin for this▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +Configurations + + +▊▔▔▔▔▔▔▔▔▎▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +▊▎Use GPUAdd GPU support to the Show help  +▊▁▁▁▁▁▁▁▁▎pipeline▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index fd6f2532c8..4d3a837545 100644 --- 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{ fill: #55c076;font-weight: bold } +.terminal-r16 { fill: #0d0d0d } +.terminal-r17 { fill: #008139 } +.terminal-r18 { fill: #ffa62b;font-weight: bold } +.terminal-r19 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊nf-core                                   ▎▊Pipeline Name▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Description▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ -▊Author(s)▎ -▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Basic details + + + + +GitHub organisationWorkflow name + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                                   ▎▊Pipeline Name▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Must be lowercase without +punctuation. + + + +A short description of your pipeline. + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Description▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊Author(s)▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index d9941b650d..875d7139cd 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,253 +19,250 @@ font-weight: 700; } - .terminal-2299823026-matrix { + .terminal-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-2299823026-title { + .terminal-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-2299823026-r1 { fill: #c5c8c6 } -.terminal-2299823026-r2 { fill: #e3e3e3 } -.terminal-2299823026-r3 { fill: #989898 } -.terminal-2299823026-r4 { fill: #98e024 } -.terminal-2299823026-r5 { fill: #626262 } -.terminal-2299823026-r6 { fill: #9d65ff } -.terminal-2299823026-r7 { fill: #fd971f } -.terminal-2299823026-r8 { fill: #e1e1e1 } -.terminal-2299823026-r9 { fill: #4ebf71;font-weight: bold } -.terminal-2299823026-r10 { fill: 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{ fill: #7ae998 } +.terminal-r13 { fill: #55c076;font-weight: bold } +.terminal-r14 { fill: #008139 } +.terminal-r15 { fill: #ffa62b;font-weight: bold } +.terminal-r16 { fill: #495259 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    -  pipelines. - -▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -▌the community as early as possible; ideally before you start on your pipeline! See the  -▌nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core +pipelines. + +▌💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +▌the community as early as possible; ideally before you start on your pipeline! See the +▌nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette From 42b55243bc5501a792b51ab75fc59d2e790961f0 Mon Sep 17 00:00:00 2001 From: yuxin ning Date: Mon, 30 Jun 2025 11:42:59 +0000 Subject: [PATCH 33/33] snapshot update from gitpod --- .../test_create_app/test_github_details.svg | 275 ++++++++++++++++++ .../test_github_exit_message.svg | 270 +++++++++++++++++ .../test_create_app/test_github_question.svg | 220 +++++++++++++- 3 files changed, 758 insertions(+), 7 deletions(-) create mode 100644 tests/pipelines/__snapshots__/test_create_app/test_github_details.svg create mode 100644 tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg new file mode 100644 index 0000000000..6c83c1497b --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -0,0 +1,275 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core pipelines create + + + + + + + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + +Now that we have created a new pipeline locally, we can create a new GitHub repository and push +the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +▊GitHub username▎▊••••••••••••                  ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + + +The name of the organisation where theThe name of the new GitHub repository +GitHub repo will be created +▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎▊▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▎ +▊nf-core                               ▎▊mypipeline                            ▎ +▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎▊▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▎ + + + +▌⚠️ You can't create a repository directly in the nf-core organisation. +▌Please create the pipeline repo to an organisation where you have access or use your user +▌account. A core-team member will be able to transfer the repo to nf-core once the development +▌has started. + +▌💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▊▔▔▔▔▔▔▔▔▎Private +▊▎Select to make the new GitHub repo private. +▊▁▁▁▁▁▁▁▁▎ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + +▏^p palette + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg new file mode 100644 index 0000000000..f28631fc53 --- /dev/null +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -0,0 +1,270 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + nf-core pipelines create + + + + + + + + + + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +If you would like to create the GitHub repository later, you can do it manually by following +these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +▌💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette + + + diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index 3804c6b773..77494c0bfe 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -1,4 +1,4 @@ - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - nf-core pipelines create + nf-core pipelines create @@ -50,9 +207,58 @@ - + - + ⭘nf-core pipelines create — Create a new pipeline with the nf-core pipeline + + +Create GitHub repository + + +After creating the pipeline template locally, we can create a GitHub repository and push the +code to it. + +Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all ▏^p palette