Dev -> Master for 3.18.0 #1476

pinin4fjords · 2024-12-20T10:15:23Z

PR checklist

TODO: - [ ] Benchmark paired ends mode - [ ] Include in multiqc

Signed-off-by: Siddhartha Bagaria <[email protected]>

Co-authored-by: Jonathan Manning <[email protected]>

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Adding differential expression analysis tutorial pages to Usage section

This reverts commit f41744e.

Bump versions to 3.18.0

…into umi_dedup_log_path

Fix log publishing around umitools/ umicollapse

nf-core-bot · 2024-12-20T10:16:01Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.0.2.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

github-actions · 2024-12-20T10:26:48Z

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

Posted for pipeline commit 324dcdf

+| ✅ 190 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
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
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: conf/igenomes_ignored.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 - 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: 3.18.0
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.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.umi_dedup_tool= umitools
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.extra_fqlint_args= --disable-validator P001
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.bracken_precision= S
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.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: 24.04.2, Config: 24.04.2
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'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
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: release-announcements.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: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: cloud_tests_full.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.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: 3.0.2
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 3.0.2
Run at 2024-12-20 16:17:14

Update from master

adamrtalbot

Give some credit to tutorial author

CHANGELOG.md

Update CHANGELOG.md

edmundmiller

LGTM!

edmundmiller · 2024-12-20T16:06:38Z

docs/usage.md

+
+By default, the pipeline will run [fq lint](https://github.com/stjude-rust-labs/fq) on all input FASTQ files, both at the start of preprocessing and after each preprocessing step that manipulates FASTQ files. If errors are found, and error will be reported and the workflow will stop.
+
+The `extra_fqlint_args` parameter can be manipulated to disable [any validator](https://github.com/stjude-rust-labs/fq?tab=readme-ov-file#validators) from `fq` you wish. For example, we have found that checks on the names of paired reads are prone to failure, so that check is disabled by default (setting `extra_fqlint_args` to `--disable-validator P001`).


I've found this too. In the next release could we set those to the default args.

siddharthab and others added 30 commits September 3, 2024 06:16

Add umicollapse as an alternative to umi-tools

fc13650

TODO: - [ ] Benchmark paired ends mode - [ ] Include in multiqc

Keep umitools as the default

761c56d

Signed-off-by: Siddhartha Bagaria <[email protected]>

add DE_analys folder

314bd76

prettier check

72e6e2e

Merge branch 'dev' into umicollapse

acd8f65

update umicollapse to 1.1.0

e86e9a6

update CHANGELOG

28b10ac

change name DE folder

6d0ebe5

modify md files

73fb0e7

prettier check

e8d8061

actually update umicollapse

e5d9d4b

Apply suggestions from code review

05513ee

Co-authored-by: Jonathan Manning <[email protected]>

Update docs/usage/DEanalysis/index.md

aa35d37

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update docs/usage/DEanalysis/interpretation.md

b1ec267

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update docs/usage/DEanalysis/rnaseq.md

659c86b

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update docs/usage/DEanalysis/rnaseq.md

f2b34d0

Co-authored-by: Matthias Hörtenhuber <[email protected]>

Update docs/usage/DEanalysis/rnaseq.md

c8c7ef8

Co-authored-by: Matthias Hörtenhuber <[email protected]>

update index.md

ae16c2c

update images

000e228

update interpretation

dfa8a04

update rnaseq

aa55fe5

update theory

f7e3c97

update de_rstudio

dbc5260

correct formula in theory

08efda6

prettier check

6be4d82

Merge pull request #1447 from LorenzoS96/dev

da5f135

Adding differential expression analysis tutorial pages to Usage section

Merge branch 'dev' into umicollapse

ee2dde2

[automated] Fix code linting

b372821

Update tests for UMICollapse module.

88d6411

Update umi-tools dedup tests at well.

15116a3

pinin4fjords and others added 19 commits December 19, 2024 11:42

Revert "Update CHANGELOG.md"

492efe9

This reverts commit f41744e.

Update changelog

0cf9100

Merge pull request #1474 from nf-core/prerelease_3.18.0

a27ec8e

Bump versions to 3.18.0

Fix minor umi dedup log issue

f67ae86

better log file fix

37b52b5

undo config change

e8459aa

tiny fix

4138270

tiny fix

16148b9

Tidy up umitools/ umicollapse config

685c1b1

update changelog

cd97229

Update UMI test

bdcd760

Update umi.nf.test

b799aa3

Exclude umi logs

6ce7096

Update outputs in docs

cb59092

Fix snapshot after log exclusion

c98f8f3

Merge branch 'umi_dedup_log_path' of https://github.com/nf-core/rnaseq …

da322f1

…into umi_dedup_log_path

Add keep intermeds to test file

311b633

Fix snapshot

0a21c3f

Merge pull request #1475 from nf-core/umi_dedup_log_path

8033764

Fix log publishing around umitools/ umicollapse

Merge branch 'master' into update_from_master

aa1ac44

pinin4fjords mentioned this pull request Dec 20, 2024

Update from master #1477

Merged

11 tasks

Merge pull request #1477 from nf-core/update_from_master

1b593f7

Update from master

adamrtalbot approved these changes Dec 20, 2024

View reviewed changes

CHANGELOG.md Show resolved Hide resolved

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pinin4fjords added 2 commits December 20, 2024 15:54

Update CHANGELOG.md

eb7d764

Merge pull request #1479 from nf-core/add_missing_changelog_entry

324dcdf

Update CHANGELOG.md

edmundmiller approved these changes Dec 20, 2024

View reviewed changes

maxulysse approved these changes Dec 20, 2024

View reviewed changes

pinin4fjords merged commit b96a753 into master Dec 20, 2024
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Dev -> Master for 3.18.0 #1476

Dev -> Master for 3.18.0 #1476

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		By default, the pipeline will run [fq lint](https://github.com/stjude-rust-labs/fq) on all input FASTQ files, both at the start of preprocessing and after each preprocessing step that manipulates FASTQ files. If errors are found, and error will be reported and the workflow will stop.

		The `extra_fqlint_args` parameter can be manipulated to disable [any validator](https://github.com/stjude-rust-labs/fq?tab=readme-ov-file#validators) from `fq` you wish. For example, we have found that checks on the names of paired reads are prone to failure, so that check is disabled by default (setting `extra_fqlint_args` to `--disable-validator P001`).

Dev -> Master for 3.18.0 #1476

Dev -> Master for 3.18.0 #1476

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pinin4fjords commented Dec 20, 2024

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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❔ Tests ignored:

✅ Tests passed:

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github-actions bot commented Dec 20, 2024 •

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