Release v2.6.0 #708

ramprasadn · 2025-06-16T09:58:01Z

PR checklist

…func

Update SVDB/merge module to fix language server problems

Replace for loop in `create_pedigree_file`

…to kubra-skip-alignment

Co-authored-by: Maxime U Garcia <[email protected]>

Template update to 3.3.1

github-actions · 2025-06-16T10:02:07Z

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

Posted for pipeline commit 390389f

+| ✅ 221 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗  28 tests had warnings |!

❗ Test warnings:

readme - README did not have a Nextflow minimum version badge.
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
_
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
_
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
_
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
_
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
_
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
_
schema_lint - Input mimetype is missing or empty
local_component_structure - annotate_structural_variants.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 - scatter_genome.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
local_component_structure - variant_evaluation.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 - call_repeat_expansions.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 - annotate_mt_snvs.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 - qc_bam.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 - annotate_genome_snvs.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 - rank_variants.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 - align.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_clinical_set.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: .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-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: nf-test.config
files_exist - File found: tests/default.nf.test
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 does not contain dev for release: 2.6.0
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.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/
nf_test_content - 'tests/default.nf.test' contains outdir parameter
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_singleton.nf.test' contains outdir parameter
nf_test_content - 'tests/test_singleton.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_singleton.nf.test' snapshots a 'versions.yml' file
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 - 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_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 nf-core template version badge found.
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_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: release-announcements.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: clean-up.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: 3.3.1
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are numeric and consistent between container, release tag and config.
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.1
Run at 2025-06-25 09:06:51

Fix issues in dev

CHANGELOG.md

README.md

maxulysse

Checking the file names in the pipeline level steps is already a super move, I love this.
Hoping we can add more later on.

kubranarci

I just have minor commends, otherwise looks all good to me

docs/usage.md

nextflow.config

subworkflows/local/align.nf

subworkflows/local/annotate_repeat_expansions.nf

subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf

tests/default.nf.test

ramprasadn and others added 30 commits October 7, 2024 13:01

add module and update schema

54d8396

run prettier

3f2fba2

add to workflow

cfc2384

Merge branch 'dev' of github.com:nf-core/raredisease into add_spring_…

231cf02

…func

update module

b82c456

Merge branch 'dev' of github.com:nf-core/raredisease into add_spring_…

0de84ed

…func

Merge branch 'dev' of github.com:nf-core/raredisease into add_spring_…

704f270

…func

Merge branch 'dev' of github.com:nf-core/raredisease into add_spring_…

8a53126

…func

Merge branch 'dev' of github.com:nf-core/raredisease into add_spring_…

2bff64c

…func

update changelog

2f544c1

add changelog

8db1af2

bump version to 2.5.0dev

b3eba09

fix testconfig

7d9bf72

skip alignment

64f09d7

temp add testbam

5a452cf

Merge branch 'dev' into skip_alignment

e359b2a

fixes one Nexflow language server issue

e860a7a

CHANGELOG

3fba6c3

Update SVDB/merge to fix language server problems

9e242ef

remove skip_alignment

c41f303

modify configs

0533ae9

modify configs

10fcc9e

update schema

2ea7e07

Merge pull request #684 from fellen31/update-svdb

6933717

Update SVDB/merge module to fix language server problems

Merge branch 'dev' into replace-for-loop

d8f8fa6

Merge pull request #683 from fellen31/replace-for-loop

df257b8

Replace for loop in `create_pedigree_file`

update docs and changelog

765dc68

Merge branch 'dev' into skip_alignment

092a5b9

fix lint

f3a852f

Merge branch 'skip_alignment' of github.com:kubranarci/raredisease in…

0cf1f3b

…to kubra-skip-alignment

ramprasadn and others added 12 commits June 11, 2025 15:43

set a vep image

7be2b98

remove sentieon

43e1cad

update configs

20aa9a7

add ngsbits to skip

99af10c

remove a test

8019402

fix lint

c6c2350

Apply suggestions from code review

2a4952e

Co-authored-by: Maxime U Garcia <[email protected]>

update spring module

9165128

Merge pull request #707 from nf-core/template-update

d076745

Template update to 3.3.1

add missing versions

91833c8

bump version

644bd33

update name in changelog

6498647

ramprasadn added 4 commits June 16, 2025 17:14

update snaps

240be93

Merge pull request #709 from nf-core/fixdev

18f0c18

Fix issues in dev

remove conda

2a23e1d

update to large disk

8f8341b

ramprasadn marked this pull request as ready for review June 17, 2025 12:00

maxulysse reviewed Jun 17, 2025

View reviewed changes

CHANGELOG.md Outdated Show resolved Hide resolved

maxulysse reviewed Jun 17, 2025

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maxulysse approved these changes Jun 17, 2025

View reviewed changes

kubranarci reviewed Jun 20, 2025

View reviewed changes

ramprasadn added 3 commits June 24, 2025 14:11

review suggestions

0472381

fix lint

7800b2f

update rocrate

b0d8f38

kubranarci approved these changes Jun 25, 2025

View reviewed changes

ramprasadn added 3 commits June 25, 2025 10:42

Update CHANGELOG.md

03d194e

Update README.md

9c3ad6c

update rocrate

390389f

ramprasadn merged commit dc7219d into master Jun 25, 2025
32 of 39 checks passed

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Release v2.6.0 #708

Release v2.6.0 #708

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ramprasadn commented Jun 16, 2025

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❗ Test warnings:

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Release v2.6.0 #708

Release v2.6.0 #708

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ramprasadn commented Jun 16, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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