Output_cn_plots_restyling by SaraPotente · Pull Request #66 · DIncalciLab/samurai

SaraPotente · 2026-07-06T08:02:30Z

Description

Adds a new module PLOT_WISECONDORX_CNV to generate copy number profile
plots for WisecondorX output, mirroring the style of PLOT_ICHORCNA.

Unlike ichorCNA, WisecondorX does not estimate tumor purity/ploidy, so
the plot stays in log2(ratio) scale (no absolute copy number correction).

Related to #60.

Changes

New module modules/local/plot_wisecondorx_cnv/ (main.nf + meta.yml)
New script bin/plot_wisecondorx_cnv.R
Integrated into LIQUID_BIOPSY subworkflow (wisecondorx branch)
New optional param plot_wisecondorx_cnv_log2ratio to configure the
y-axis clipping range (--ratio_limit)

PR checklist

github-actions · 2026-07-06T08:05:30Z

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

Posted for pipeline commit cbba41d

+| ✅ 255 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: 1.4.0
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.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.wisecondorx_plot_y_max= 1.0
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
nextflow_config - Config default value correct: params.cin_segmentMean_tai= 0.2
nextflow_config - Config default value correct: params.cin_segmentMean_cna= 0.2
nextflow_config - Config default value correct: params.cin_segmentMean_base_segments= 0.2
nextflow_config - Config default value correct: params.cin_segmentMean_break_points= 0.2
nextflow_config - Config default value correct: params.cin_segmentMean_fga= 0.2
nextflow_config - Config default value correct: params.cin_segmentDistance_cna= 10000000.0
nextflow_config - Config default value correct: params.cin_minSegSize_cna= 1000000.0
nextflow_config - Config default value correct: params.cin_genomeSize_fga= 2873203431.0
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: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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 - FORMAT_ICHORCNA_SEG 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 - PLOT_WISECONDORX_CNV 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 - COMPUTE_CINMETRICS 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 = 1.4.0, nfcore_yml.version = 1.4.0

Run details

nf-core/tools version 3.4.1
Run at 2026-07-07 08:06:37

lbeltrame · 2026-07-06T11:12:33Z

Looks mostly OK, with a few minor nits.

lbeltrame

LGTM!

SaraPotente added 4 commits July 6, 2026 09:54

add module for plotting wisecondorx cnv

adfa920

add R script for plotting wisecondorx cnv

a0fe366

add plot_wisecondorx_cnv to liquid_biopsy wf

1647996

update config

5ad65ac

update comments

f21ee72

lbeltrame requested changes Jul 6, 2026

View reviewed changes

Comment thread conf/modules.config

Comment thread subworkflows/local/liquid_biopsy/main.nf

Comment thread nextflow.config Outdated

SaraPotente added 6 commits July 6, 2026 14:36

update nextflow_schema

d5fcede

update nextflow.config

932308a

fix params description

a25d289

update modules.config

443dd33

fix schema value

d367313

update parameter name and description

cbba41d

lbeltrame approved these changes Jul 7, 2026

View reviewed changes

lbeltrame merged commit dfc204f into master Jul 7, 2026
4 checks passed

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Output_cn_plots_restyling#66

Output_cn_plots_restyling#66
lbeltrame merged 11 commits into
masterfrom
output_cn_plots_restyling

SaraPotente commented Jul 6, 2026

Uh oh!

github-actions Bot commented Jul 6, 2026 •

edited

Loading

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

lbeltrame commented Jul 6, 2026

Uh oh!

lbeltrame left a comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

Uh oh!

Conversation

SaraPotente commented Jul 6, 2026

Description

Changes

PR checklist

Uh oh!

github-actions Bot commented Jul 6, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Uh oh!

Uh oh!

Uh oh!

lbeltrame commented Jul 6, 2026

Uh oh!

lbeltrame left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

2 participants

github-actions Bot commented Jul 6, 2026 •

edited

Loading

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