[skip ci] Dev -> Master for 3.15.0 #1258

drpatelh · 2024-03-12T10:31:49Z

Adds nf-test to all components of pipeline
Improvements to reporting in MultiQC, in particular to strandedness
Use factored-out preprocessing subworkflow from nf-core
Documentation updates
Separate indexing step in sortmerna to speed things up

github-actions · 2024-03-12T10:34:39Z

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

Posted for pipeline commit 8446cbc

+| ✅ 172 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   8 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
files_exist - File not found: .github/workflows/awstest.yml
files_exist - File not found: .github/workflows/awsfulltest.yml
nextflow_config - Config manifest.version should end in dev: 3.15.0
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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

files_exist - File is ignored: conf/modules.config
nextflow_config - Config default ignored: params.ribo_database_manifest
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
multiqc_config - multiqc_config
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-rnaseq_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-rnaseq_logo_light.png
files_exist - File found: docs/images/nf-core-rnaseq_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: 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-rnaseq_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/WorkflowRnaseq.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 - 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: params.validationShowHiddenParams
nextflow_config - Config variable found: params.validationSchemaIgnoreParams
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 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 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.hisat2_build_memory= 200.GB
nextflow_config - Config default value correct: params.gtf_extra_attributes= gene_name
nextflow_config - Config default value correct: params.gtf_group_features= gene_id
nextflow_config - Config default value correct: params.featurecounts_group_type= gene_biotype
nextflow_config - Config default value correct: params.featurecounts_feature_type= exon
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.trimmer= trimgalore
nextflow_config - Config default value correct: params.min_trimmed_reads= 10000
nextflow_config - Config default value correct: params.umitools_extract_method= string
nextflow_config - Config default value correct: params.umitools_grouping_method= directional
nextflow_config - Config default value correct: params.aligner= star_salmon
nextflow_config - Config default value correct: params.pseudo_aligner_kmer_size= 31
nextflow_config - Config default value correct: params.min_mapped_reads= 5.0
nextflow_config - Config default value correct: params.kallisto_quant_fraglen= 200
nextflow_config - Config default value correct: params.kallisto_quant_fraglen_sd= 200
nextflow_config - Config default value correct: params.stranded_threshold= 0.8
nextflow_config - Config default value correct: params.unstranded_threshold= 0.1
nextflow_config - Config default value correct: params.deseq2_vst= true
nextflow_config - Config default value correct: params.rseqc_modules= bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication
nextflow_config - Config default value correct: params.skip_bbsplit= true
nextflow_config - Config default value correct: params.skip_preseq= true
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.max_cpus= 16
nextflow_config - Config default value correct: params.max_memory= 128.GB
nextflow_config - Config default value correct: params.max_time= 240.h
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/7f1614baeb0ddf66e60be78c3d9fa55440465ac8/
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/sendmail_template.txt matches the template
files_unchanged - assets/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnaseq_logo_dark.png matches the template
files_unchanged - docs/README.md matches the template
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
readme - README Zenodo placeholder was replaced with DOI.
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (571 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: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: ci.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: release-announcements.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found in modules.json
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
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: 2.14.1

Run details

nf-core/tools version 2.14.1
Run at 2024-09-04 10:31:22

.github/python/find_changed_files.py

…onfig.

…in the General Stats table of MultiQC.

… logs.

…d 'umi_log' and not 'log'. The meta.yml is wrong.

…onfiguration parameters used in the config were deprecated.

maxulysse · 2024-08-29T15:05:21Z

Missing one PR in CHANGELOG + fixing typos

Clarify output files: - add gene_lengths description - clarify that scaled output files contain estimated counts from abundances

Clarify design formula and blind dispersion estimation

Clarify docs on different tximport count files

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

…nto prerelease_3.15.0_fixes

Bump versions for 3.15.0

Apply Maxime's changelog edits

Bump tximeta/tximport for gene table row names fix

maxulysse · 2024-09-05T08:10:04Z

@sguizard all good for you?

sguizard · 2024-09-05T08:13:18Z

To the best of my knowledge, looks OK to me.

pinin4fjords · 2024-09-05T08:42:30Z

Thank you @sguizard !

adamrtalbot reviewed Apr 18, 2024

View reviewed changes

.github/python/find_changed_files.py Outdated Show resolved Hide resolved

maxulysse and others added 28 commits July 3, 2024 11:06

add stubs + code polish + Harshil align

573ca90

add stub

3efcb84

update all nf-core modules and subworkflows and do not include tags

345d1f8

simplify snapshot for stub

eb08f2f

add stubs for subworkflow local quantify_rsem

c956f6f

update default snapshot

bf5797f

Modify FastQC output publishing to comply with the paths in MultiQC c…

a2443e7

…onfig.

MultiQC config updates.

00d6113

Linting.

7dade35

Use the correct module names to supress the Percent Duplicate column …

1bf9390

…in the General Stats table of MultiQC.

Publish logfiles from umi-tools dedup steps.

850cb4c

Modify subworkflow bam_dedup_stats_samtools_umitools to publish dedup…

2cb8eff

… logs.

Update bam_dedup_stats_samtools_umitools subworkflow and MultiQC module.

6648b35

Add UMI information for Watchmaker mRNA Library Prep Kit.

2924f9e

Publish the UMI-tools extract logs for MultiQC.

8a4aa8a

The output channel of fastq_fastqc_umitools_trimgalore/fastp is calle…

af1b91c

…d 'umi_log' and not 'log'. The meta.yml is wrong.

Mark FASTQC outputs with suffixes

df31182

@aanil (Anandashankar Anil) correctly pointed out that some MultiQC c…

8bca15a

…onfiguration parameters used in the config were deprecated.

Linting

6178e8c

Changelog

4dc5b67

add plugin

37780ad

update all subworkflows

150ac0b

do not snapshot fastq in stub

9fd07da

pipeline level stub

2cdeea1

fix stub test for prepare_genome

3c78a6a

update all subworkflows

c572fc0

correctly align

df9efba

Use nf-core/setup-nf-test action for portability

3edd994

pinin4fjords and others added 23 commits September 3, 2024 14:11

Update docs/output.md

d78a5d6

Update docs/output.md

4f0aa71

Update output.md

803e02d

Clarify output files: - add gene_lengths description - clarify that scaled output files contain estimated counts from abundances

Update CHANGELOG.md

144c11f

Remove restatement of params defaults

6450fbf

Update CHANGELOG.md

760e83f

Apply suggestions from code review

dff00b6

Merge pull request #1367 from pmoris/clarify-deseq2-qc

1190e6c

Clarify design formula and blind dispersion estimation

Merge branch 'dev' into improve-docs-count-files

3587b18

Merge pull request #1366 from pmoris/improve-docs-count-files

0d93da5

Clarify docs on different tximport count files

Bump versions

a266448

Bump modules

65162d4

Remove tags from tests

b4d3735

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

Fix version in snapshot

9b1c08a

Merge branch 'prerelease_3.15.0_fixes' of github.com:nf-core/rnaseq i…

fb38827

…nto prerelease_3.15.0_fixes

Merge pull request #1370 from nf-core/prerelease_3.15.0_fixes

349ad86

Bump versions for 3.15.0

Apply Maxime's suggestions to changelog

9fc9a35

Add new PRs to changelog

90a1e83

Bump CI

2b32127

Merge pull request #1371 from nf-core/maxime_changelog_changes

e73c741

Apply Maxime's changelog edits

Bump tximeta/tximport for gene table rownames fix

11f0c73

Update changelog

59988f8

Merge pull request #1372 from nf-core/bump_tximport_gene_names

8446cbc

Bump tximeta/tximport for gene table row names fix

maxulysse approved these changes Sep 4, 2024

View reviewed changes

sguizard approved these changes Sep 5, 2024

View reviewed changes

pinin4fjords merged commit 4e34945 into master Sep 5, 2024
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[skip ci] Dev -> Master for 3.15.0 #1258

[skip ci] Dev -> Master for 3.15.0 #1258

drpatelh commented Mar 12, 2024 •

edited by pinin4fjords

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github-actions bot commented Mar 12, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Aug 29, 2024

maxulysse commented Sep 5, 2024

sguizard commented Sep 5, 2024

pinin4fjords commented Sep 5, 2024

[skip ci] Dev -> Master for 3.15.0 #1258

[skip ci] Dev -> Master for 3.15.0 #1258

Conversation

drpatelh commented Mar 12, 2024 • edited by pinin4fjords Loading

github-actions bot commented Mar 12, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

maxulysse commented Aug 29, 2024

maxulysse commented Sep 5, 2024

sguizard commented Sep 5, 2024

pinin4fjords commented Sep 5, 2024

drpatelh commented Mar 12, 2024 •

edited by pinin4fjords

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github-actions bot commented Mar 12, 2024 •

edited

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