Release 2.2.0 #127

edmundmiller · 2025-05-30T16:10:25Z

Fresh release from #124 and #126

Template update for nf-core/tools version 2.14.0

Co-authored-by: Anders Sune Pedersen <[email protected]>

Important! Template update for nf-core/tools v2.14.1

Update samtools to 1.19.2 in local module CHECK_IF_PAIRED_END

update samtools

Add fastqutils/info to check for truncated or quality-mismatched files

* Prepare release 2.2.0 * Prettier

* remove whitespace from subway map * fix citations * changelog * remove more whitespace * copy nf-test file from rnavar * revert some changes

github-actions · 2025-05-30T16:11:45Z

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

Posted for pipeline commit 3d1e65b

+| ✅ 242 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

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 base.config: Check the defaults for all processes
local_component_structure - check_paired_end.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
local_component_structure - prepare_indices.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - alignment_to_fastq.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
local_component_structure - pre_conversion_qc.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/ci.yml
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore

✅ 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-bamtofastq_logo_light.png
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/images/nf-core-bamtofastq_logo_light.png
files_exist - File found: docs/images/nf-core-bamtofastq_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-bamtofastq_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/WorkflowBamtofastq.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: 2.2.0
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.reads_in_memory= 100000
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.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
nf_test_content - 'tests/collate_fast.nf.test' contains outdir parameter
nf_test_content - 'tests/collate_fast.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/collate_fast.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chr.nf.test' contains outdir parameter
nf_test_content - 'tests/chr.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/chr.nf.test' snapshots a 'versions.yml' file
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/cram.nf.test' contains outdir parameter
nf_test_content - 'tests/cram.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/cram.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_bai.nf.test' contains outdir parameter
nf_test_content - 'tests/no_bai.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_bai.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_stats.nf.test' contains outdir parameter
nf_test_content - 'tests/no_stats.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_stats.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_qc.nf.test' contains outdir parameter
nf_test_content - 'tests/no_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_crai.nf.test' contains outdir parameter
nf_test_content - 'tests/no_crai.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/no_crai.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/CONTRIBUTING.md 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/PULL_REQUEST_TEMPLATE.md 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 - assets/nf-core-bamtofastq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bamtofastq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-bamtofastq_logo_dark.png matches the template
files_unchanged - docs/README.md 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 Nextflow minimum version badge matched config. Badge: 24.04.2, Config: 24.04.2
readme - README nf-core template version badge found.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_if_empty_null - No ifEmpty(null) 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_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
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: fix_linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: template-version-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: nf-test.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: release-announcements.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'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - FASTQC_PRE_CONVERSION found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_POST_CONVERSION found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_COLLATEFASTQ_SINGLE_END found in conf/modules.config and Nextflow scripts.
modules_config - COLLATE_FASTQ_MAP found in conf/modules.config and Nextflow scripts.
modules_config - COLLATE_FASTQ_UNMAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_MAP_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FLAGSTAT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_IDXSTATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_MAP_UNMAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_UNMAP_MAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_VIEW_UNMAP_UNMAP found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_MERGE_UNMAP found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - CHECK_IF_PAIRED_END found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_CHR 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: 3.3.1
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 2025-06-03 10:02:34

Important! Template update for nf-core/tools v3.3.1

nf-core-bot and others added 30 commits May 8, 2024 13:58

Template update for nf-core/tools version 2.14.0

24dd736

Merge branch 'dev' into nf-core-template-merge-2.14.0

4106d54

Adding fasta and fasta_fai to the list validationSchemaIgnoreParams

4532a4f

Fixing path to test data

f1561e8

Fixing editing mistake

80d3ed6

Template update for nf-core/tools version 2.14.1

e83eacc

Back to dev

0bd0628

Update changelog

7b05538

Back to dev with nf-core bump-version 2.1.2dev

714d622

Removing CUSTOM_DUMPSOFTWAREVERSIONS from config

7b7e031

Merge pull request #90 from asp8200/nf-core-template-merge-2.14.0

e729868

Template update for nf-core/tools version 2.14.0

Merge branch 'dev' into nf-core-template-merge-2.14.1

fec0fcb

[automated] Fix code linting

4920f9b

fix DOI

eca1593

fix linting

517d9d9

fix linting

0381ee2

Update CHANGELOG.md

1d872ef

Co-authored-by: Anders Sune Pedersen <[email protected]>

Merge pull request #91 from nf-core/nf-core-template-merge-2.14.1

3e672f8

Important! Template update for nf-core/tools v2.14.1

Update samtools to 1.19.2 in local module CHECK_IF_PAIRED_END

6ba2518

Updating the changelog

dc14ba6

Fix typo

0c16b07

Fix typo

c96a296

Remove comment

e62fab4

Merge pull request #93 from asp8200/update_local_module

34c06a7

Update samtools to 1.19.2 in local module CHECK_IF_PAIRED_END

update samtools

41d0bcc

update samtools in local module

9b036a6

update changelog

e6b01fe

Merge pull request #94 from asp8200/update_samtools

5961440

update samtools

Template update for nf-core/tools version 3.0.0

f2fd239

Template update for nf-core/tools version 3.0.1

699fd19

famosab and others added 12 commits May 19, 2025 15:48

fix snapshot

60af5c2

update subway map

2658850

update docs

abc75d0

update docs

4ba31c6

update docs - fix font size

082db37

move png

0bb209c

add comment

3a01d97

update readme

b047e3b

Merge pull request #120 from famosab/fastqutils

a35d8cf

Add fastqutils/info to check for truncated or quality-mismatched files

Codeowners (#122)

567bfc3

Prepare release 2.2.0 (#123)

ee7e630

* Prepare release 2.2.0 * Prettier

Address review comments for release 2.2.0 (#125)

afd86e1

* remove whitespace from subway map * fix citations * changelog * remove more whitespace * copy nf-test file from rnavar * revert some changes

edmundmiller assigned famosab May 30, 2025

edmundmiller added this to the 2.2.0 milestone May 30, 2025

edmundmiller added this to PRs to master May 30, 2025

github-project-automation bot moved this to Todo in PRs to master May 30, 2025

edmundmiller moved this from Todo to In Progress in PRs to master May 30, 2025

FriederikeHanssen approved these changes May 30, 2025

View reviewed changes

nf-core-bot and others added 8 commits June 2, 2025 14:43

Template update for nf-core/tools version 3.3.1

c0cfbb5

Merge branch 'dev' into nf-core-template-merge-3.3.1

3be7da9

Update .nf-core.yml

79afbfe

Update rocrate and add missing param

90c1e52

fix lint

16e1386

fix modules versions

0d31a76

update fastqutils

d45b984

Merge pull request #128 from nf-core/nf-core-template-merge-3.3.1

3d1e65b

Important! Template update for nf-core/tools v3.3.1

famosab approved these changes Jun 16, 2025

View reviewed changes

edmundmiller merged commit 8698321 into master Jun 16, 2025
67 of 68 checks passed

github-project-automation bot moved this from In Progress to Done in PRs to master Jun 16, 2025

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Release 2.2.0 #127

Release 2.2.0 #127

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edmundmiller commented May 30, 2025

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❗ Test warnings:

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✅ Tests passed:

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Release 2.2.0 #127

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edmundmiller commented May 30, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented May 30, 2025 •

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