Release 2.0.0 #184

scwatts · 2025-04-10T03:18:34Z

No description provided.

* add source selection for RNA BAM (samplesheet, alignment subworkflow) * use appropriate function call to determine present of RNA * relocate isofox_read_length assignment (wgts and targeted workflows)

- allow custom panels with config 'force_panel' - UMI duplex UMI delimiter with config 'umi_duplex_delim' - UMI extraction from fastq with config 'umi_length'

Fix utilisation of user-provided BamTools directory

Apply minor fixes and updates

Set COBALT pcg_gamma argument when running in targeted mode

Update pipeline version text displayed in the ORANGE report

Update documentation

Prepare release 2.0.0

Enable loading custom pipeline config

github-actions · 2025-04-10T03:20:09Z

`nf-core pipelines lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 9f93f51

+| ✅ 199 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  16 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
schema_params - Schema param panel not found from nextflow config
schema_params - Schema param fastp_umi_location not found from nextflow config
schema_params - Schema param fastp_umi_length not found from nextflow config
schema_params - Schema param fastp_umi_skip not found from nextflow config
schema_params - Schema param redux_umi_duplex_delim not found from nextflow config
schema_params - Schema param genome_version not found from nextflow config
schema_params - Schema param genome_type not found from nextflow config
schema_params - Schema param ref_data_hmf_data_path not found from nextflow config
schema_params - Schema param ref_data_panel_data_path not found from nextflow config
schema_params - Schema param ref_data_genome_gtf not found from nextflow config
schema_params - Schema param ref_data_hla_slice_bed not found from nextflow config

❔ Tests ignored:

files_exist - File is ignored: lib/Utils.groovy
files_exist - File is ignored: lib/WorkflowMain.groovy
files_exist - File is ignored: lib/WorkflowOncoanalyser.groovy
nextflow_config - Config default ignored: params.fastp_umi_length
nextflow_config - Config default ignored: params.fastp_umi_skip
files_unchanged - File ignored due to lint config: assets/nf-core-oncoanalyser_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-oncoanalyser_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-oncoanalyser_logo_dark.png
actions_ci - actions_ci
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
files_exist - File found: .prettierignore
files_exist - File found: .prettierrc.yml
files_exist - File found: CHANGELOG.md
files_exist - File found: CITATIONS.md
files_exist - File found: CODE_OF_CONDUCT.md
files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_exist - File found: nextflow_schema.json
files_exist - File found: nextflow.config
files_exist - File found: README.md
files_exist - File found: .github/.dockstore.yml
files_exist - File found: .github/CONTRIBUTING.md
files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
files_exist - File found: .github/workflows/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-oncoanalyser_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-oncoanalyser_logo_light.png
files_exist - File found: docs/images/nf-core-oncoanalyser_logo_dark.png
files_exist - File found: docs/output.md
files_exist - File found: docs/README.md
files_exist - File found: docs/README.md
files_exist - File found: docs/usage.md
files_exist - File found: main.nf
files_exist - File found: conf/base.config
files_exist - File found: conf/igenomes.config
files_exist - File found: conf/igenomes_ignored.config
files_exist - File found: .github/workflows/awstest.yml
files_exist - File found: .github/workflows/awsfulltest.yml
files_exist - File found: modules.json
files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
files_exist - File not found check: .github/workflows/push_dockerhub.yml
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
files_exist - File not found check: bin/markdown_to_html.r
files_exist - File not found check: conf/aws.config
files_exist - File not found check: docs/images/nf-core-oncoanalyser_logo.png
files_exist - File not found check: lib/Checks.groovy
files_exist - File not found check: lib/Completion.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: Singularity
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
nextflow_config - Found nf-schema plugin
nextflow_config - Config variable found: manifest.name
nextflow_config - Config variable found: manifest.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
nextflow_config - Config variable found: manifest.homePage
nextflow_config - Config variable found: timeline.enabled
nextflow_config - Config variable found: trace.enabled
nextflow_config - Config variable found: report.enabled
nextflow_config - Config variable found: dag.enabled
nextflow_config - Config variable found: process.cpus
nextflow_config - Config variable found: process.memory
nextflow_config - Config variable found: process.time
nextflow_config - Config variable found: params.outdir
nextflow_config - Config variable found: params.input
nextflow_config - Config variable found: validation.help.enabled
nextflow_config - Config variable found: manifest.mainScript
nextflow_config - Config variable found: timeline.file
nextflow_config - Config variable found: trace.file
nextflow_config - Config variable found: report.file
nextflow_config - Config variable found: dag.file
nextflow_config - Config variable found: validation.help.beforeText
nextflow_config - Config variable found: validation.help.afterText
nextflow_config - Config variable found: validation.help.command
nextflow_config - Config variable found: validation.summary.beforeText
nextflow_config - Config variable found: validation.summary.afterText
nextflow_config - Config variable (correctly) not found: params.nf_required_version
nextflow_config - Config variable (correctly) not found: params.container
nextflow_config - Config variable (correctly) not found: params.singleEnd
nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
nextflow_config - Config variable (correctly) not found: params.name
nextflow_config - Config variable (correctly) not found: params.enable_conda
nextflow_config - Config variable (correctly) not found: params.max_cpus
nextflow_config - Config variable (correctly) not found: params.max_memory
nextflow_config - Config variable (correctly) not found: params.max_time
nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found: params.validationLenientMode
nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
nextflow_config - Config timeline.enabled had correct value: true
nextflow_config - Config report.enabled had correct value: true
nextflow_config - Config trace.enabled had correct value: true
nextflow_config - Config dag.enabled had correct value: true
nextflow_config - Config manifest.name began with nf-core/
nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
nextflow_config - Config dag.file ended with .html
nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
nextflow_config - Config manifest.version does not contain dev for release: 2.0.0
nextflow_config - Config params.custom_config_version is set to master
nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profile test
nextflow_config - Config default value correct: params.force_genome= false
nextflow_config - Config default value correct: params.force_panel= false
nextflow_config - Config default value correct: params.prepare_reference_only= false
nextflow_config - Config default value correct: params.create_stub_placeholders= false
nextflow_config - Config default value correct: params.max_fastq_records= 10000000
nextflow_config - Config default value correct: params.fastp_umi= false
nextflow_config - Config default value correct: params.redux_umi= false
nextflow_config - Config default value correct: params.isofox_functions= TRANSCRIPT_COUNTS;ALT_SPLICE_JUNCTIONS;FUSIONS;RETAINED_INTRONS
nextflow_config - Config default value correct: params.igenomes_ignore= true
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.hmf_genomes_base= https://pub-cf6ba01919994c3cbd354659947f74d8.r2.dev/genomes
nextflow_config - Config default value correct: params.custom_config_version= master
nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Config default value correct: params.publish_dir_mode= copy
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/oncoanalyser
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/CONTRIBUTING.md matches the template
files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
files_unchanged - .github/workflows/branch.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
files_unchanged - .github/workflows/linting.yml matches the template
files_unchanged - assets/email_template.html matches the template
files_unchanged - assets/email_template.txt matches the template
files_unchanged - assets/sendmail_template.txt matches the template
files_unchanged - docs/README.md matches the template
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (0 files)
schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - WRITE_REFERENCE_DATA found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - REDUX found in conf/modules.config and Nextflow scripts.
modules_config - AMBER found in conf/modules.config and Nextflow scripts.
modules_config - COBALT found in conf/modules.config and Nextflow scripts.
modules_config - PURPLE found in conf/modules.config and Nextflow scripts.
modules_config - BAMTOOLS found in conf/modules.config and Nextflow scripts.
modules_config - CHORD found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACTCONTIG found in conf/modules.config and Nextflow scripts.
modules_config - LILAC found in conf/modules.config and Nextflow scripts.
modules_config - SIGS found in conf/modules.config and Nextflow scripts.
modules_config - VIRUSBREAKEND found in conf/modules.config and Nextflow scripts.
modules_config - VIRUSINTERPRETER found in conf/modules.config and Nextflow scripts.
modules_config - ISOFOX found in conf/modules.config and Nextflow scripts.
modules_config - NEO_SCORER found in conf/modules.config and Nextflow scripts.
modules_config - NEO_FINDER found in conf/modules.config and Nextflow scripts.
modules_config - CUPPA found in conf/modules.config and Nextflow scripts.
modules_config - ORANGE found in conf/modules.config and Nextflow scripts.
nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 3.0.2
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.0.2
Run at 2025-04-10 04:47:50

Fix the download pipeline CI/CD

docs/usage/faq_and_troubleshooting.md

jfy133 · 2025-04-10T06:49:19Z

@scwatts quick question - is this PR going for an official release?

If so, while it's great you got two reviews - we strongly encourage that at least one of the reviewers is 'external' from the project/same employer. This is to ensure that an 'isolated bubble' forms of styles/patterns starts forming. This has happened in the past and the results were not pretty (pipelines very diverged from template/guidelines etc, which caused knock-on effects downstream in future template updates/reviews etc).

If you've not done the actual GitHub release yet, it would be great if you could ask on #release-review-trading to trade with someone else to help keep things in check (And use that in the future)

ohofmann · 2025-04-10T12:03:44Z

Following up on @jfy133 's comment so it doesn't get lost -- we missed the requirement for an external reviewer in this PR review process. Absolutely makes sense and we'll work with the nf-core community to have a reviewer or two on standby (and contribute to other reviews in the meantime, about to join the review-trading channel). Apologies again!

scwatts and others added 30 commits February 1, 2024 15:15

Frame out Neo subworkflow

90a3a78

First cut of Neoepitope subworkflow

4913bb8

Get stub runs working

396e01a

Set Neo to run only when specified

7abbccb

Update Neo reference data paths

01563bc

Provide Neo cancer type from samplesheet

801ec4d

Move neo_prediction.nf subworkflow for consistency

d31a929

Adjust Neo to fit with alignment subworkflow

cd3c2de

* add source selection for RNA BAM (samplesheet, alignment subworkflow) * use appropriate function call to determine present of RNA * relocate isofox_read_length assignment (wgts and targeted workflows)

Custom panel support with TWIST UMIs:

8fe4a6b

- allow custom panels with config 'force_panel' - UMI duplex UMI delimiter with config 'umi_duplex_delim' - UMI extraction from fastq with config 'umi_length'

Fixed force_panel check

e5e2a26

Fixed type in umi length default

fa88861

Fixed UMI length argument

e7313ab

Run UMIs if duplex delimiter or length is specified

6eea2e9

Only set fastp split_by_lines argument when needed

bc33179

Indent Neo subworkflow to match nf-core style

2e4a57a

Use Bioconda for Neo annotate fusion process

9be8491

Add environment file for annotate fusion process

c2e15ea

Rename some Neo subworkflow variables for clarity

5085556

Add meta.yml files for processes related to Neo

8a488db

Add donor sample support

66387d7

Update input definition for donor MarkDups BAM

825c3d5

Automatically detect ref_sample_count in SAGE_SOMATIC process

f4ebd78

Cast normal/donor bam to string in SAGE_SOMATIC

7fc7c8b

Check if normal_id/donor_id exists using not null

aa5c670

Enable SAGE append when Neo is set to run

93ab007

Linx somatic writes neoepitopes

175a7d7

Add reference to Neo in documentation

ef7db8c

Minor formatting adjustments

0233911

Targeted workflow can now accept a normal/reference sample.

f653e40

Refactor for dev aims, linting

60894a9

scwatts and others added 17 commits April 6, 2025 08:45

Update CHANGELOG.md

dd9572d

Link out to GH issue for details of known issues

9b17402

Merge pull request #176 from nf-core/fix-bamtools-existing-input-check

cb30d5b

Fix utilisation of user-provided BamTools directory

Merge pull request #178 from nf-core/general-fixes-and-updates

41cee55

Apply minor fixes and updates

Adjust pipeline version in the ORANGE report

9013399

Configure COBALT pcf_gamma when in targeted mode

ad85cff

Merge pull request #180 from nf-core/set-targeted-cobalt-pcf-gamma

57d2da0

Set COBALT pcg_gamma argument when running in targeted mode

Merge pull request #179 from nf-core/update-orange-pipeline-version-text

1ae73ec

Update pipeline version text displayed in the ORANGE report

Apply Hartwig documentation changes

efca716

Adjust documentation

9dbd6a5

Fix and improve documentation

5557d04

Apply doc feedback, fix link, remove admonition

edb26b7

Merge pull request #181 from nf-core/update-documentation

397550e

Update documentation

Bump to 2.0.0

fffdc7f

Merge pull request #182 from nf-core/prepare-release-2.0.0

cac2582

Prepare release 2.0.0

Uncomment custom pipeline config import statement

c473599

Merge pull request #183 from nf-core/enable-pipeline-custom-configs

8d639e7

Enable loading custom pipeline config

scwatts requested review from ohofmann, charlesshale and luan-n-nguyen April 10, 2025 03:18

luan-n-nguyen approved these changes Apr 10, 2025

View reviewed changes

scwatts and others added 2 commits April 10, 2025 14:22

Remove stub-alternative in pipeline download CI/CD

0390545

Merge pull request #185 from nf-core/fix-download-pipeline-cicd

9f93f51

Fix the download pipeline CI/CD

charlesshale approved these changes Apr 10, 2025

View reviewed changes

maxulysse reviewed Apr 10, 2025

View reviewed changes

docs/usage/faq_and_troubleshooting.md Show resolved Hide resolved

scwatts mentioned this pull request Apr 10, 2025

Review docs to identify sections appropriate for the main nf-core website #186

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scwatts merged commit d1218d2 into master Apr 10, 2025
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Release 2.0.0 #184

Release 2.0.0 #184

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scwatts commented Apr 10, 2025

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✅ Tests passed:

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jfy133 commented Apr 10, 2025

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ohofmann commented Apr 10, 2025

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Release 2.0.0 #184

Release 2.0.0 #184

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scwatts commented Apr 10, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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jfy133 commented Apr 10, 2025

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`nf-core pipelines lint` overall result: Passed ✅ ⚠️