Update ichorCNA to the nf-core upstream versions by lbeltrame · Pull Request #57 · DIncalciLab/samurai

lbeltrame · 2025-11-18T14:11:29Z

This PR updates the ichorCNA modules to their upstream versions and updates to the latest available version in nf-core (0.5.1).

Cf. #34

PR checklist

lbeltrame · 2025-11-18T14:12:54Z

CI is failing due to the currently-ongoing Cloudlflare issue
Moving the PoN generation to a samplesheet format is also planned in this PR.

This updates the samplesheet in preparation of DIncalciLab/samurai#57.

github-actions · 2025-11-19T10:10:15Z

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

Posted for pipeline commit 9736ba4

+| ✅ 243 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
pipeline_todos - TODO string in main.nf.test: Once you have added the required tests, please run the following command to build this file:
pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/samurai/samurai/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ path(versions.yml) ]
_

❔ Tests ignored:

files_exist - File is ignored: CODE_OF_CONDUCT.md
files_exist - File is ignored: assets/samurai_logo_mqc.png
files_exist - File is ignored: assets/nf-core-samurai_logo_light.png
files_exist - File is ignored: docs/images/nf-core-samurai_logo_light.png
files_exist - File is ignored: docs/images/nf-core-samurai_logo_dark.png
files_exist - File is ignored: docs/images/samurai_logo.png
files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
files_exist - File is ignored: .github/workflows/awstest.yml
files_exist - File is ignored: .github/workflows/awsfulltest.yml
files_exist - File is ignored: .github/workflows/ci.yml
files_exist - File is ignored: .github/workflows/branch.yml
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: .github/actions/get-shards/action.yml
files_exist - File is ignored: .github/actions/nf-test/action.yml
files_exist - File is ignored: nf-test.config
files_exist - File is ignored: tests/default.nf.test
files_exist - File is ignored: ro-crate-metadata.json
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File does not exist: assets/nf-core-samurai_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-samurai_logo_light.png
files_unchanged - File does not exist: docs/images/nf-core-samurai_logo_dark.png
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_nf_test - '.github/workflows/nf-test.yml' not found
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/samurai/samurai/.github/workflows/awstest.yml
schema_params - schema_params
rocrate_readme_sync - ro-crate-metadata.json not found
included_configs - included_configs

✅ 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: 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/feature_request.yml
files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
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: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: assets/multiqc_config.yml
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: 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-samurai_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/Utils.groovy
files_exist - File not found check: lib/Workflow.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/WorkflowSamurai.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.nextflowVersion
nextflow_config - Config variable found: manifest.description
nextflow_config - Config variable found: manifest.version
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: 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 (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 variable (correctly) not found: validation.failUnrecognisedParams
nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
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 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: 1.3.1
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.genome= hg38
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes
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.max_multiqc_email_size= 25.MB
nextflow_config - Config default value correct: params.validate_params= true
nextflow_config - Config default value correct: params.purity= 1
nextflow_config - Config default value correct: params.title= Fragment size distribution
nextflow_config - Config default value correct: params.max_fragmentsize= 400
nextflow_config - Config default value correct: params.binsize= 500
nextflow_config - Config default value correct: params.caller= qdnaseq
nextflow_config - Config default value correct: params.analysis_type= solid_biopsy
nextflow_config - Config default value correct: params.qdnaseq_paired_ends= true
nextflow_config - Config default value correct: params.pon_name= PoN
nextflow_config - Config default value correct: params.selection_maxsize= 150
nextflow_config - Config default value correct: params.ichorcna_genome_style= UCSC
nextflow_config - Config default value correct: params.ichorcna_readcounter_chrs= chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22
nextflow_config - Config default value correct: params.ichorcna_readcounter_quality= 20
nextflow_config - Config default value correct: params.ichorcna_chrs_to_use= 1:22
nextflow_config - Config default value correct: params.ichorcna_chrs_to_train= 1:22
nextflow_config - Config default value correct: params.ichorcna_chrs_to_normalize= 1:22
nextflow_config - Config default value correct: params.ichorcna_estimate_normal= true
nextflow_config - Config default value correct: params.ichorcna_fraction_reads_male= 0.001
nextflow_config - Config default value correct: params.ichorcna_male_chrX_logR= 0.3
nextflow_config - Config default value correct: params.ichorcna_min_map_score= 0.75
nextflow_config - Config default value correct: params.ichorcna_max_frac_genome_subclone= 0.5
nextflow_config - Config default value correct: params.ichorcna_max_frac_cna_subclone= 0.7
nextflow_config - Config default value correct: params.ichorcna_min_segment_bins= 50
nextflow_config - Config default value correct: params.ichorcna_max_cn= 5
nextflow_config - Config default value correct: params.ichorcna_txne= 0.9999
nextflow_config - Config default value correct: params.ichorcna_alt_frac_threshold= 0.05
nextflow_config - Config default value correct: params.ichorcna_trx_strength= 10000
nextflow_config - Config default value correct: params.ichorcna_plotfiletype= pdf
nextflow_config - Config default value correct: params.ichorcna_plotylim= -2,4
nextflow_config - Config default value correct: params.ichorcna_estimate_ploidy= true
nextflow_config - Config default value correct: params.ichorcna_normal_states= 0.5, 0.6, 0.7, 0.8, 0.9, 0.95, 0.99
nextflow_config - Config default value correct: params.wisecondorx_yfrac= 0.4
nextflow_config - Config default value correct: params.wisecondorx_zscore= 5
nextflow_config - Config default value correct: params.ascat_sc_predict_refit= TRUE
nextflow_config - Config default value correct: params.ascat_sc_segmentation_alpha= 0.01
nextflow_config - Config default value correct: params.ascat_sc_min_purity= 0.01
nextflow_config - Config default value correct: params.ascat_sc_max_purity= 1
nextflow_config - Config default value correct: params.ascat_sc_min_ploidy= 1.7
nextflow_config - Config default value correct: params.ascat_sc_max_ploidy= 5
nextflow_config - Config default value correct: params.ascat_sc_max_tumor_ploidy= 5
nextflow_config - Config default value correct: params.gistic_t_amp= 0.1
nextflow_config - Config default value correct: params.gistic_t_del= 0.1
nextflow_config - Config default value correct: params.gistic_conf= 0.99
nextflow_config - Config default value correct: params.gistic_qval= 0.05
nextflow_config - Config default value correct: params.gistic_broad_chr_length= 0.99
nextflow_config - Config default value correct: params.gistic_cn_cap= 6
nextflow_config - Config default value correct: params.fastp_cut_window_size= 4
nextflow_config - Config default value correct: params.hrdcna_threshold= 0.2
nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'nf-test.config' sets a testsDir
nf_test_content - 'nf-test.config' sets a workDir
nf_test_content - 'nf-test.config' sets a configFile
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml 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/feature_request.yml matches the template
files_unchanged - .github/PULL_REQUEST_TEMPLATE.md 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
readme - README Zenodo placeholder was replaced with DOI.
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: ci.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.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
multiqc_config - assets/multiqc_config.yml found and not ignored.
multiqc_config - assets/multiqc_config.yml contains report_section_order
multiqc_config - assets/multiqc_config.yml contains export_plots
multiqc_config - assets/multiqc_config.yml contains report_comment
multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
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 - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - BWAMEM2_MEM found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX_SIZE_SELECTION found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS_PRE found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS_POST found in conf/modules.config and Nextflow scripts.
modules_config - BAMPE_FRAGMENTSIZE_PRE found in conf/modules.config and Nextflow scripts.
modules_config - BAMPE_FRAGMENTSIZE_POST found in conf/modules.config and Nextflow scripts.
modules_config - QDNASEQ found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_QDNASEQ_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - HMMCOPY_READCOUNTER_ICHORCNA found in conf/modules.config and Nextflow scripts.
modules_config - HMMCOPY_READCOUNTER_PON found in conf/modules.config and Nextflow scripts.
modules_config - ICHORCNA_CREATEPON found in conf/modules.config and Nextflow scripts.
modules_config - ICHORCNA_RUN found in conf/modules.config and Nextflow scripts.
modules_config - AGGREGATE_ICHORCNA_TABLE found in conf/modules.config and Nextflow scripts.
modules_config - CORRECT_LOGR_ICHORCNA found in conf/modules.config and Nextflow scripts.
modules_config - PLOT_ICHORCNA found in conf/modules.config and Nextflow scripts.
modules_config - CONCATENATE_QDNASEQ_PLOTS found in conf/modules.config and Nextflow scripts.
modules_config - NORMAL_CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - WISECONDORX_CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - WISECONDORX_NEWREF found in conf/modules.config and Nextflow scripts.
modules_config - WISECONDORX_PREDICT found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_GISTIC_SEG found in conf/modules.config and Nextflow scripts.
modules_config - ASSEMBLE_WISECONDORX_OUTPUTS found in conf/modules.config and Nextflow scripts.
modules_config - CONVERT_WISECONDORX_IMAGES found in conf/modules.config and Nextflow scripts.
modules_config - ASCAT_SC found in conf/modules.config and Nextflow scripts.
modules_config - CONCATENATE_BIN_PLOTS found in conf/modules.config and Nextflow scripts.
modules_config - CONCATENATE_ASCATSC_PLOTS found in conf/modules.config and Nextflow scripts.
modules_config - CONCATENATE_ASCATSC_REFITTED_PLOTS found in conf/modules.config and Nextflow scripts.
modules_config - CREATE_ASCATSC_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - CIN_SIGNATURE_QUANTIFICATION found in conf/modules.config and Nextflow scripts.
modules_config - HRDCNA found in conf/modules.config and Nextflow scripts.
modules_config - GISTIC2 found in conf/modules.config and Nextflow scripts.
modules_config - ASSEMBLE_GISTIC_OUTPUT found in conf/modules.config and Nextflow scripts.
modules_config - MAFTOOLS 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: 3.4.1
version_consistency - Version tags are consistent: manifest.version = 1.3.1, nfcore_yml.version = 1.3.1

Run details

nf-core/tools version 3.4.1
Run at 2025-12-10 07:56:56

**BREAKING CHANGE**: this changes the format parameters for ichorCNA

lbeltrame · 2025-11-20T13:01:11Z

Pushed a "defensive" change against ichorCNA's liberal handling of inputs. The downside is that some of the ichorcna* parameters will change format, so we need to make sure this is spelt clear.

lbeltrame · 2025-12-02T13:24:56Z

Not a blocker, but GavinHaLab/ichorCNA#26 wold be good to have (although that requires either a new ichorCNA version, or bioconda/bioconda-recipes#61045 to be merged)

lbeltrame · 2025-12-09T09:04:54Z

The bioconda PR has been merged, so I need to create a new container and push the update to nf-core. To speed things up we can use the patch functionality of nf-core to use the newer container ASAP.

lbeltrame · 2025-12-10T07:32:56Z

All good on my side. @SaraPotente please check if there are any blockers. I'll update the changelog in the mean time, then if all is well, merge and cut a new release.

lbeltrame added 4 commits November 18, 2025 14:42

Mport the ichorCNA modules

15919fa

Port the option handling to the newer ichorCNA modules

dbb44da

Finish porting to the newer ichorCNA modules

088a8a2

Remove local ichorCNA modules

f3e0c43

lbeltrame requested a review from SaraPotente November 18, 2025 14:11

lbeltrame added a commit to DIncalciLab/samurai-test-data that referenced this pull request Nov 19, 2025

Add status column to samplesheet.csv

7254672

This updates the samplesheet in preparation of DIncalciLab/samurai#57.

lbeltrame mentioned this pull request Nov 19, 2025

Add status column to samplesheet.csv DIncalciLab/samurai-test-data#1

Merged

Plumbing to support PoN samples in the samplesheet directly

92f928f

lbeltrame added 2 commits November 19, 2025 11:18

Remove configuration for modules that no longer exist

d2b7d9f

Act defensively when supplying ichorCNA parameters

9c2730d

**BREAKING CHANGE**: this changes the format parameters for ichorCNA

Convert "string booleans" to proper bools

33c9287

lbeltrame mentioned this pull request Nov 20, 2025

Switch to upstream nf-core modules where possible #34

Open

2 tasks

lbeltrame added 14 commits November 20, 2025 14:39

Port the remnants of the configuration

a8080e4

Update default in schema

e1cf0a2

Convert the workflow to the use of PoN in the samplesheet

a4f6770

Fix option type

1471bc3

Don't consume the aligner index after first use

3af75b6

Use actually the correct file

24f39fe

Switch container image to the polars-based CLI tool

d462530

Use the right column name

e664f75

The quest for the right column ID continues...

ba848bc

Fix another column namee

baa1f35

Fix dashes vs underscores

456b6b7

remove all references to pon_path

7653eca

Better error message

ed1cb14

Add a trailing "," to args

3957a02

lbeltrame self-assigned this Dec 9, 2025

lbeltrame added 4 commits December 10, 2025 07:45

Try to collect all samples for WisecondorX

0cb46e8

Update the ichorCNA modules to add the fix for chrX

674e90d

Actually fix WisecondorX PoN

7e3bfb0

CIn signatures: don't plot if there's only one sample (#59)

d7514a9

lbeltrame marked this pull request as ready for review December 10, 2025 07:32

Update documentation and CHANGELOG

9736ba4

lbeltrame merged commit f4aeaaf into master Dec 10, 2025
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Update ichorCNA to the nf-core upstream versions#57

Update ichorCNA to the nf-core upstream versions#57
lbeltrame merged 27 commits intomasterfrom
update-ichorcna

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

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