Update CI workflows #52

lbeltrame · 2025-10-24T07:42:57Z

This PR was open exactly to test them.

github-actions · 2025-10-24T08:33:17Z

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

Posted for pipeline commit aac3b5b

+| ✅ 220 tests passed       |+
#| ❔  24 tests were ignored |#
!| ❗  20 tests had warnings |!

❗ Test warnings:

files_exist - File not found: conf/igenomes_ignored.config
files_exist - File not found: ro-crate-metadata.json
nextflow_config - nf-validation has been detected in the pipeline. Please migrate to nf-schema: https://nextflow-io.github.io/nf-schema/latest/migration_guide/
readme - README did not have an nf-core template version badge.
pipeline_todos - TODO string in base.config: Check the defaults for all processes
pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
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) ]
_
schema_description - No description provided in schema for parameter: purity
schema_description - No description provided in schema for parameter: max_fragmentsize
schema_description - No description provided in schema for parameter: ichorcna_male_chrX_logR
schema_description - No description provided in schema for parameter: ichorcna_filter_bam_pon
schema_description - No description provided in schema for parameter: wisecondorx_yfrac
schema_description - No description provided in schema for parameter: ascat_sc_max_tumor_ploidy
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ 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: nf-test.config
files_exist - File is ignored: .github/actions/nf-test/action.yml
files_exist - File is ignored: .github/actions/get-shards/action.yml
files_exist - File is ignored: .github/workflows/nf-test.yml
files_exist - File is ignored: tests/default.nf.test
nextflow_config - Config variable ignored: manifest.name
nextflow_config - Config variable ignored: manifest.homePage
nf_test_content - nf_test_content
files_unchanged - Required pipeline config not found - {'manifest.contributors'}
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

✅ 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: 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-validation 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 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: 1.2.3.1
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= paste0('chr', c(1:22))
nextflow_config - Config default value correct: params.ichorcna_chrs_to_train= paste0('chr', c(1:22))
nextflow_config - Config default value correct: params.ichorcna_chrs_to_normalize= paste0('chr', c(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_include_homd= FALSE
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= c(-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
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.
base_config - CUSTOM_DUMPSOFTWAREVERSIONS found in conf/base.config and Nextflow scripts.
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_GENERATE_PON found in conf/modules.config and Nextflow scripts.
modules_config - RUN_ICHORCNA 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.
modules_config - CUSTOM_DUMPSOFTWAREVERSIONS 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 = 1.2.3.1, nfcore_yml.version = 1.2.3.1

Run details

nf-core/tools version 3.4.1
Run at 2025-10-31 14:05:19

lbeltrame · 2025-10-31T14:02:03Z

This can't be fixed until the other refactoring is complete.

lbeltrame closed this Oct 24, 2025

lbeltrame force-pushed the update-ci branch from 4539f8c to c3d17b8 Compare October 24, 2025 07:51

Update CI actions

7cff2e2

lbeltrame reopened this Oct 24, 2025

lbeltrame added 4 commits October 24, 2025 09:54

Fix typo

28201cd

Fix copy-paste errors

8f16770

Fix hashes

af54003

Fix wrong hash (verified)

46b2de4

lbeltrame added 9 commits October 24, 2025 13:54

Try to fix lint

647d16c

Use the workflows for the template

f671346

Fix one lint

4ffca4d

Bump nf-core versions

dfa1182

More CI fixes

57e8c20

Update utils_nfcore_pipeline

47debc8

Update modules.json

7f8baac

Update the rest, oops

9767d0f

Fix nf-core YML

1c450e7

Remove non-existent functions

aac3b5b

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Update CI workflows #52

Update CI workflows #52

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lbeltrame commented Oct 24, 2025

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edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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lbeltrame commented Oct 31, 2025

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lbeltrame commented Oct 24, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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lbeltrame commented Oct 31, 2025

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github-actions bot commented Oct 24, 2025 •

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