Release 2.2.0 by scwatts · Pull Request #243 · nf-core/oncoanalyser

scwatts · 2025-08-26T06:20:49Z

No description provided.

… same as BAM/BAM_REDUX/BAI files

…lude run processes excluded by default

… resource creation workflows

Co-authored-by: Stephen Watts <scwatts@users.noreply.github.com>

…y from workflow.manifest.version

…ionableCodingPanel and CoverageCodingPanel files

…_path

Add reports to tower.yml

Force install of compatible icu version 73.2, the newer 75.1 version available in conda-forge can be installed with older the r-stringr and r-stringi recipes but is incompatible.

…or-fastq-data Support relative paths for fastq data

All WiGiTS tools that accept the log_level argument support the 'OFF' value except CHORD, which causes oncoanalyser to crash. Therefore, this log_level / hmftools_log_level value is not allowed.

Apply minor fixes and updates

Prepare release 2.2.0

github-actions · 2025-08-26T06:22:27Z

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

Posted for pipeline commit dedcbe7

+| ✅ 217 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗  17 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
schema_description - No description provided in schema for parameter: prepare_reference_only

❔ 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: 2.2.0
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.create_stub_placeholders= false
nextflow_config - Config default value correct: params.max_fastq_records= 10000000
nextflow_config - Config default value correct: params.fastp_umi_enabled= false
nextflow_config - Config default value correct: params.redux_umi_enabled= 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.hmftools_log_level= DEBUG
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.prepare_reference_only= false
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: 24.10.5, Config: 24.10.5
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: linting_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: nf-test.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 - WISP 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.
modules_config - COBALT_PANEL_NORMALISATION found in conf/modules.config and Nextflow scripts.
modules_config - PAVE_PON_PANEL_CREATION found in conf/modules.config and Nextflow scripts.
modules_config - ISOFOX_PANEL_NORMALISATION 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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 2.2.0, nfcore_yml.version = 2.2.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-02 02:05:34

danilodileo

The pipeline looks well written and organised. I read through the files but I haven't spend too much time since I am not familiar with most of the tools implemented here.
I am testing the pipeline and I will let you know if I encounter major errors/issues.

I have just few comments:

As I understood you only have one nf-test for stub mode. shouldn't be good to include more?
You have many modules in local. it would be good to consider to move some of them in nf-core/modules since other developers might find it useful.
nf-core AWS fill size tests fail. it needs to be fixed

great job!

The GH Action self-hosted RunsOn instances do not have sufficient disk space to execute non-stub tests (currently 80 GB of EBS volume according to these docs: https://runs-on.com/configuration/job-labels/#disk). Also using nf-test tags as providing paths to desired tests is not honoured when --changed-since is supplied.

Reviewer recommendations and other adjustments

scwatts · 2025-09-02T05:28:02Z

Thank you for the review @danilodileo!

I've now added the test profile as a new nf-test case. The reason this wasn't initially done is that the GH Action automatically executes all tests, and the runner instances don't have sufficient disk space to store the reference data needed for the test profile (the stub run is configured in such a way that no reference data is required). In order to handle this, I've also set the corresponding GH Action to only execute the stub run; the new test can otherwise be run with nf-test test or similar

We're happy to explore making these tools more easily accessible to the community, though in their current state they are strongly interdependent on one another and running them in a standalone way isn't really possible, so the modules aren't individually that useful to others

I confirmed the AWS full sized test is also failing (though only on manual trigger), and this appears to be caused by some unspecified error during submission of the Seqera Platform job. Looks like it's a known issue with the current advice to ask someone from the nf-core team to trigger the job once the release is completed

scwatts · 2025-09-02T05:45:25Z

The newly failing GH Action workflow that runs nf-core pipelines download is hitting an error because it uses nf-core/tools from the latest commit on the dev branch and there has recently been a refactor / rework of this feature merged into dev, which appears to have introduced a fatal bug

I have manually tested the nf-core pipelines download command with the most recent release of nf-core/tools (3.3.2; i.e. prior to the download feature refactor) on the changes in this release PR both locally and on another branch (check-tools-download; GH Action job), and each test finished successfully

To confirm this wasn't related to oncoanalyser itself, I also built a minimal reproducible example. See here for more information:

Pipeline download feature does not appear to handle Docker image conversion correctly tools#3742

Since the nf-core pipelines download command does work for the changes in this PR when using a release version rather than development version, I will proceed with this release instead of waiting for a fix to be pushed to the dev branch of nf-core/tools

ohofmann

I am okay with the proposed changes — thanks for all the work (and the external reviewers).

scwatts and others added 30 commits June 4, 2024 16:52

Add modules for WISP workflow

8b825d3

Implement relevant subworkflows for WISP workflow

eefb45d

Add WISP workflow

be99938

Add modules for panel resource creation workflow

0952d84

Input / parameter handling for WISP workflow

0d5ee7b

Convert ESVEE to a single module

79644d5

Add options for prepare reference only mode

f9f00cb

Add CLI arg ref_data_types and remove arg prepare_reference_only

a82e02a

Add new mode prepare_reference

eac906b

Implement panel resource creation subworkflows

be890ad

Add panel resource creation workflow

c5bdf3a

Add module_log_level param to control all WiGiTS module log levels

3c9cade

Add CRAM/CRAM_REDUX/CRAI filetypes. Internally, these are treated the…

bdb566c

… same as BAM/BAM_REDUX/BAI files

Remove unused input file type REDUX_DUP_FREQ_TSV

1a1e7a0

Update HMF tools arguments

ccf93d6

Implement purity estimate mode type

bb23bd6

Adjust workflow and subworkflow for new HMF tool arguments

dfd61a6

Apply WISP workflow updates and fixes

d332229

Apply fixes and updates

7a6c758

add reports to tower.yml

b846b0d

add folder structure

7b3aefd

Apply logging argument to remaining HMF tools

b9a7832

Make processes_manual run specified processes, and make processes_inc…

58d19be

…lude run processes excluded by default

Provide prep config to prepare reference in purity estimate and panel…

d8f2f27

… resource creation workflows

Run NEO by default

b8b0399

Apply suggestions from code review

9fdcaa5

Co-authored-by: Stephen Watts <scwatts@users.noreply.github.com>

When determining prepare_reference output dir, get git branch directl…

c74ec79

…y from workflow.manifest.version

In panel resource creation, remove gene-utils call to create SAGE Act…

d09b2df

…ionableCodingPanel and CoverageCodingPanel files

Add option to override default driver_gene_panel in ref_data_hmf_data…

a3cb777

…_path

Merge pull request #220 from FriederikeHanssen/reporting

66f2759

Add reports to tower.yml

scwatts and others added 13 commits August 13, 2025 21:26

Apply fixes, cleanup to SAGE processes

a66a93d

Handle more FASTQ, longitudinal sample input cases

8af7868

Reintroduce use of decoy sequence images for ESVEE

8492c2d

Set min stringr stringi version for CUPPA

99c040d

Force install of compatible icu version 73.2, the newer 75.1 version available in conda-forge can be installed with older the r-stringr and r-stringi recipes but is incompatible.

Merge pull request #229 from alexiswl/bugfix/support-relative-paths-f…

cb620c4

…or-fastq-data Support relative paths for fastq data

Allow prepare reference through standard modes

b381f59

Set and use input paths for panel resource creation

e011cde

Disallow 'OFF' hmftools_log_level value

fa392ae

All WiGiTS tools that accept the log_level argument support the 'OFF' value except CHORD, which causes oncoanalyser to crash. Therefore, this log_level / hmftools_log_level value is not allowed.

Update CHANGELOG.md

08c3a19

Bump to 2.2.0

21c3417

Add note about CRAM requirements

6e8e9d7

Merge pull request #241 from nf-core/general-updates-and-fixes

2e5bc8a

Apply minor fixes and updates

Merge pull request #242 from nf-core/prepare-release-2.2.0

5359570

Prepare release 2.2.0

scwatts requested a review from danilodileo August 26, 2025 06:35

danilodileo reviewed Aug 27, 2025

View reviewed changes

Comment thread README.md

danilodileo reviewed Aug 27, 2025

View reviewed changes

Comment thread docs/usage.md

danilodileo reviewed Aug 27, 2025

View reviewed changes

Comment thread docs/usage/faq_and_troubleshooting.md

Fix check for multiple longitudinal sample entries

d15aa12

danilodileo approved these changes Aug 28, 2025

View reviewed changes

scwatts and others added 5 commits September 1, 2025 17:31

Allow test profile to be run by nf-test

b4d2202

Update README.md with reviewer feedback

afbaf92

Update, fix documentation

5cdf451

Merge pull request #245 from nf-core/review-and-other-adjustments

dedcbe7

Reviewer recommendations and other adjustments

scwatts requested a review from ohofmann September 2, 2025 05:59

ohofmann approved these changes Sep 2, 2025

View reviewed changes

scwatts merged commit b94cbc7 into master Sep 2, 2025
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Release 2.2.0#243

Release 2.2.0#243
scwatts merged 92 commits into
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scwatts commented Aug 26, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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✅ Tests passed:

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

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