Merge master (2.5.0) to dev #704

ramprasadn · 2025-05-23T08:11:42Z

PR checklist

…to patch

…o concat_mt_genome

concatenate nuclear and mt SNV calls

Add Verifybamid2

github-actions · 2025-05-23T08:13:13Z

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

Posted for pipeline commit c442334

+| ✅ 202 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  21 tests had warnings |!

❗ Test warnings:

schema_lint - Input mimetype is missing or empty
local_component_structure - call_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - qc_bam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - scatter_genome.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_mt_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - call_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_structural_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - rank_variants.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_repeat_expansions.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - gens.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - generate_cytosure_files.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - call_snv.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - variant_evaluation.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - prepare_references.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - subsample_mt.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - align.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_consequence_pli.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - generate_clinical_set.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - annotate_genome_snvs.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - call_mobile_elements.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
modules_config - modules_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/ci.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-raredisease_logo_light.png
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
files_exist - File found: docs/images/nf-core-raredisease_logo_light.png
files_exist - File found: docs/images/nf-core-raredisease_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: 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: .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-raredisease_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/WorkflowRaredisease.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 ends in dev: 2.6.0dev
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.bait_padding= 100
nextflow_config - Config default value correct: params.genome= GRCh38
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.mito_name= chrM
nextflow_config - Config default value correct: params.analysis_type= wgs
nextflow_config - Config default value correct: params.extract_alignments= false
nextflow_config - Config default value correct: params.platform= illumina
nextflow_config - Config default value correct: params.ngsbits_samplegender_method= xy
nextflow_config - Config default value correct: params.scatter_count= 20
nextflow_config - Config default value correct: params.aligner= bwamem2
nextflow_config - Config default value correct: params.mt_aligner= bwamem2
nextflow_config - Config default value correct: params.samtools_sort_threads= 4
nextflow_config - Config default value correct: params.mbuffer_mem= 3072
nextflow_config - Config default value correct: params.min_trimmed_length= 40
nextflow_config - Config default value correct: params.mt_subsample_rd= 150
nextflow_config - Config default value correct: params.mt_subsample_seed= 30
nextflow_config - Config default value correct: params.cnvnator_binsize= 1000
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.variant_caller= deepvariant
nextflow_config - Config default value correct: params.variant_type= snp,indel
nextflow_config - Config default value correct: params.vep_cache_version= 112
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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - CODE_OF_CONDUCT.md matches the template
files_unchanged - LICENSE matches the template
files_unchanged - .github/.dockstore.yml 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/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_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 24.04.4, Config: 24.04.4
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO 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_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
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 a matching 'report_comment'.
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 modules directory structure is correct 'modules/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
base_config - NFCORE_RAREDISEASE found in conf/base.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: 3.2.1

Run details

nf-core/tools version 3.2.1
Run at 2025-05-23 08:29:29

ramprasadn and others added 30 commits April 22, 2025 17:01

update vcf2cytosure input logic

4cb85c7

Update date in CHANGELOG.md

d3f43ef

concatenate calls

29e48af

update ci

91ce5e4

Update CHANGELOG.md

d354c05

Template update for nf-core/tools version 3.2.1

aff6910

Merge remote-tracking branch 'origin/nf-core-template-merge-3.2.1' in…

eab8ca7

…to patch

Merge branch 'patch' of github.com:nf-core/raredisease into patch

938330d

review suggestion

35358f8

Merge branch 'concat_mt_genome' of github.com:nf-core/raredisease int…

221b125

…o concat_mt_genome

Merge branch 'patch' into concat_mt_genome

290a162

Merge pull request #699 from nf-core/concat_mt_genome

ffab51c

concatenate nuclear and mt SNV calls

lint

76f155a

update version

b60aab2

update link

a516f0f

add verifybamid

2ed8a9e

update module with stub

d4055b2

update metromaps

4300637

update docs & add module to multiqc report

b03d134

updatae changelog

bbbbf6e

review suggestions

a6f08a6

fix lint

11b3d73

update parameter name

793fe48

add citations

cb97ec0

Merge pull request #701 from nf-core/verifybamid2

0ca26c1

Add Verifybamid2

add mitochondria-mode arg to filtermutect2

537e71e

Update postprocess_MT_calls.config

b39add1

change prefix for cram files

58be010

update login in cytosure swf

44a1449

update date

608a2e6

ramprasadn added 2 commits May 23, 2025 10:05

Merge branch 'patch' of github.com:nf-core/raredisease into bumpversion

d76e82b

Trigger CI tests

74f21f3

ramprasadn added 3 commits May 23, 2025 10:24

update

936a37b

fix lint

69f7990

update multiqc comment

c442334

ramprasadn marked this pull request as ready for review May 23, 2025 08:50

ramprasadn merged commit ccdfbd9 into dev May 23, 2025
9 checks passed

ramprasadn deleted the bumpversion branch June 25, 2025 08:53

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Merge master (2.5.0) to dev #704

Merge master (2.5.0) to dev #704

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ramprasadn commented May 23, 2025

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github-actions bot commented May 23, 2025 •

edited

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Merge master (2.5.0) to dev #704

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ramprasadn commented May 23, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

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github-actions bot commented May 23, 2025 •

edited

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