Implement Neo subworkflow #116

scwatts · 2024-12-05T01:13:54Z

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)

github-actions · 2024-12-05T01:15:26Z

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

Posted for pipeline commit 8b15c62

+| ✅ 197 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  14 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
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 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_virusbreakenddb_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
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 ends in dev: 1.1.0dev
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.prepare_reference_only= false
nextflow_config - Config default value correct: params.create_stub_placeholders= 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 - assets/nf-core-oncoanalyser_logo_light.png matches the template
files_unchanged - docs/images/nf-core-oncoanalyser_logo_light.png matches the template
files_unchanged - docs/images/nf-core-oncoanalyser_logo_dark.png 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: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.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 - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - MARKDUPS 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_ 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 - SAMTOOLS_FLAGSTAT 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

Run details

nf-core/tools version 3.0.2
Run at 2024-12-05 01:15:06

Stephen Watts and others added 17 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)

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

Enable SAGE append when Neo is set to run

93ab007

Linx somatic writes neoepitopes

175a7d7

Add reference to Neo in documentation

ef7db8c

Do not run SAGE append germline for Neo

8b15c62

scwatts requested a review from charlesshale December 5, 2024 01:13

charlesshale approved these changes Dec 5, 2024

View reviewed changes

scwatts merged commit f029bec into dev Dec 5, 2024
6 checks passed

scwatts deleted the implement-neo-subworkflow branch December 5, 2024 22:18

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Implement Neo subworkflow #116

Implement Neo subworkflow #116

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scwatts commented Dec 5, 2024

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scwatts commented Dec 5, 2024

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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