Release 2.1.0 by scwatts · Pull Request #215 · nf-core/oncoanalyser

scwatts · 2025-06-11T06:30:27Z

No description provided.

Additionally, switch to Bioconda package and BioContainers images

Post release bump

See https://nfcore.slack.com/archives/C04QR0T3G3H/p1745504826926699

Downgrade nf-schema to 2.2.0

- the fastp split_by_lines argument value is calculated from max_fastq_records - max_fastq_records values greater or equal to 536,870,912 (2 ^ 32 / 2 / 4) cause an integer overflow - this is fixed by casting max_fastq_records to Long type before calculating the value for split_by_lines

Fix integer overflow of fastp --split_by_lines value

Fix REDUX TSV discovery for non-local files

github-actions · 2025-06-11T06:32:06Z

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

Posted for pipeline commit 1282615

+| ✅ 212 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  16 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_unchanged - LICENSE does not match the template
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
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!
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
nf_test_content - nf_test_content
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
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: .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/nf-test.yml
files_exist - File found: .github/actions/get-shards/action.yml
files_exist - File found: .github/actions/nf-test/action.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: nf-test.config
files_exist - File found: tests/default.nf.test
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 found: ro-crate-metadata.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: 2.1.0
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 - .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_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
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
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) strings found
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template-version-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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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 - CIDER 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 - TEAL 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 - PEACH 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: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
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 3.3.1
Run at 2025-06-30 02:39:40

maxulysse

minor comments

… workflow and process. Set custom -pcf_gamma value for targeted + tumor-only mode

…ed mode

Fix targeted mode parameters

There is now no change in nf-schema version between the 2.0.0 and 2.1.0 releases.

When the link is not anchored it is rendered without the 'usage' component: 'https://nf-co.re/oncoanalyser/dev/docs/faq_and_troubleshooting'. Hence, to fix the full URL is set.

Reviewer recommendations and other adjustments

Add metromap-style diagram for pipeline overview

maxulysse

Looking good.

Still some deviations from the nf-core standards, but nothing blocking a release from me.

scwatts and others added 30 commits November 6, 2024 16:08

Continue PEACH implementation from e9bd36a

ec11829

Bump PEACH to 2.0.0

24b61d5

Additionally, switch to Bioconda package and BioContainers images

Add PEACH subworkflow

ff33b1b

Call PEACH in wgts workflow

c57c74c

Update PEACH reference data

0609b08

Fix link for FAQ

fc6d5ac

Improve SAGE somatic stub

77cf9ab

Use consistent input var names in PURPLE module

0f00c61

Template update for nf-core/tools version 3.2.1

995949a

Post-release bump

a491fae

Merge pull request #199 from nf-core/post-release-bump

59af640

Post release bump

Downgrade nf-schema to 2.2.0 as recommended

0be8e5e

See https://nfcore.slack.com/archives/C04QR0T3G3H/p1745504826926699

Merge pull request #200 from nf-core/downgrade-nf-schema

380699d

Downgrade nf-schema to 2.2.0

Update CHANGELOG.md

fbf8e64

Update CHANGELOG.md

ea0276c

Merge pull request #190 from nf-core/fix-fastp-argument-integer-overflow

3431e40

Fix integer overflow of fastp --split_by_lines value

Correct index name in usage.md

430a484

Fix SAGE meta.yml REDUX TSV entries

5c949ce

Fix REDUX TSV discovery for non-local files

608f758

Update CHANGELOG.md

2b88f15

Merge pull request #201 from nf-core/fix-redux-tsv-discovery

067e21a

Fix REDUX TSV discovery for non-local files

Adjust spacing and alignment for consistency

ea7af7a

Prevent use of incompatible CUPPA output in ORANGE

af55664

Fix error message formatting

020441a

Fix prepared reference data directory names

870c336

Update PAVE container directive to v1.7.1

b372906

Update SAGE germline PON and update PON filter in PAVE

96155a6

Add PEACH to targeted mode

f8f4278

Update documentation

6cd1a4e

maxulysse reviewed Jun 11, 2025

View reviewed changes

Comment thread nextflow.config

maxulysse reviewed Jun 11, 2025

View reviewed changes

Comment thread nextflow.config

maxulysse reviewed Jun 11, 2025

View reviewed changes

Comment thread docs/usage.md Outdated

maxulysse requested changes Jun 11, 2025

View reviewed changes

luan-n-nguyen and others added 16 commits June 17, 2025 10:57

Delete targeted_parameters.config and instead pass run mode to COBALT…

9f73b44

… workflow and process. Set custom -pcf_gamma value for targeted + tumor-only mode

Get run mode at COBALT process level using Utils.getEnumFromString()

ef93fc8

Add -high_depth_mode to SAGE germline and append processes for target…

7e7615d

…ed mode

Update CHANGELOG.md

b9a6b13

Merge pull request #217 from nf-core/fix-targeted-mode-parameters

847658b

Fix targeted mode parameters

Fix usage.md links to process and filetype lists

bed2ead

Remove nf-schema entry from CHANGELOG.md

7fb09aa

There is now no change in nf-schema version between the 2.0.0 and 2.1.0 releases.

Update CHANGELOG.md with release date

c594a4a

Update usage.md FAQ link

92a6a84

When the link is not anchored it is rendered without the 'usage' component: 'https://nf-co.re/oncoanalyser/dev/docs/faq_and_troubleshooting'. Hence, to fix the full URL is set.

Make use / documentation of NF args consistent

e873d38

Fix custom profile includes

5986346

Merge pull request #218 from nf-core/review-and-other-adjustments

ac773b2

Reviewer recommendations and other adjustments

Add metromap-style diagram for pipeline overview

840dee9

Update CHANGELOG.md

b318a1c

Use original layout for pipeline overview diagram

434bc69

Merge pull request #219 from nf-core/add-pipeline-metromap

8819838

Add metromap-style diagram for pipeline overview

maxulysse reviewed Jun 24, 2025

View reviewed changes

Comment thread docs/images/oncoanalyser_pipeline.png

maxulysse reviewed Jun 24, 2025

View reviewed changes

Comment thread nextflow.config

maxulysse reviewed Jun 24, 2025

View reviewed changes

Comment thread nf-test.config

maxulysse approved these changes Jun 25, 2025

View reviewed changes

scwatts commented Jun 30, 2025

View reviewed changes

Comment thread CHANGELOG.md Outdated

Update CHANGELOG.md with 2.1.0 release date

1282615

scwatts requested a review from charlesshale June 30, 2025 02:37

charlesshale approved these changes Jun 30, 2025

View reviewed changes

scwatts merged commit 0d0dc25 into master Jun 30, 2025
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Release 2.1.0#215

Release 2.1.0#215
scwatts merged 98 commits into
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scwatts commented Jun 11, 2025

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scwatts commented Jun 11, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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github-actions Bot commented Jun 11, 2025 •

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