Dev -> Master for 3.21.0 #1607

pinin4fjords · 2025-09-18T11:49:39Z

This release is dedicated almost entirely to two recent PRs which add BAM input functionality to RNAseq, and move the STAR alignment out of the RSEM process so that it's more visible and controllable. Everything else is just fallout from that- e.g. we have to configure STAR differently if its results are going to Salmon or STAR.

PR checklist

Bump version back to dev after release 3.20.0

…alignment

…entry_point

Enable BAM input for RSEM

…form

Fix default for umi_discard_read to prevent validation errors in Platform

Bump version to 3.21.0 ahead of release

github-actions · 2025-09-18T11:52:46Z

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

Posted for pipeline commit 13c6e21

+| ✅ 292 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   9 tests had warnings |!

❗ Test warnings:

files_exist - File not found: assets/multiqc_config.yml
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
pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
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_if_empty_null - ifEmpty(null) found in main.nf: _ versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ]
_

❔ 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
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: .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-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: nf-test.config
files_exist - File found: tests/default.nf.test
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: .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-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: 3.21.0
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/
nf_test_content - 'tests/remove_ribo_rna.nf.test' contains outdir parameter
nf_test_content - 'tests/remove_ribo_rna.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/remove_ribo_rna.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/remove_ribo_rna.nf.test' contains outdir parameter
nf_test_content - 'tests/remove_ribo_rna.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/remove_ribo_rna.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star_rsem.nf.test' contains outdir parameter
nf_test_content - 'tests/star_rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star_rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star_rsem.nf.test' contains outdir parameter
nf_test_content - 'tests/star_rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/star_rsem.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_default.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_default.nf.test' contains outdir parameter
nf_test_content - 'tests/sentieon_default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/sentieon_default.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bam_input.nf.test' contains outdir parameter
nf_test_content - 'tests/bam_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bam_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bam_input.nf.test' contains outdir parameter
nf_test_content - 'tests/bam_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/bam_input.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_trimming.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_trimming.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_qc.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_qc.nf.test' contains outdir parameter
nf_test_content - 'tests/skip_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/skip_qc.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' contains outdir parameter
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/kallisto.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' contains outdir parameter
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.nf.test' contains outdir parameter
nf_test_content - 'tests/salmon.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/salmon.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/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/min_mapped_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/min_mapped_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/min_mapped_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/min_mapped_reads.nf.test' contains outdir parameter
nf_test_content - 'tests/min_mapped_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/min_mapped_reads.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' contains outdir parameter
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/hisat2.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nofasta.nf.test' contains outdir parameter
nf_test_content - 'tests/nofasta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/nofasta.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/featurecounts_group_type.nf.test' contains outdir parameter
nf_test_content - 'tests/featurecounts_group_type.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/featurecounts_group_type.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/featurecounts_group_type.nf.test' contains outdir parameter
nf_test_content - 'tests/featurecounts_group_type.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/featurecounts_group_type.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.nf.test' contains outdir parameter
nf_test_content - 'tests/umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.nf.test' contains outdir parameter
nf_test_content - 'tests/umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.nf.test' contains outdir parameter
nf_test_content - 'tests/umi.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/umi.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/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
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: 24.10.5, Config: 24.10.5
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_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_comment.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: cloud_tests_small.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: awsfulltest.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: cloud_tests_full.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: nf-test.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'
local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.
version_consistency - Version tags are consistent: manifest.version = 3.21.0, nfcore_yml.version = 3.21.0
included_configs - Pipeline config includes custom configs.

Run details

nf-core/tools version 3.3.2
Run at 2025-09-18 11:52:27

maxulysse · 2025-09-18T12:04:15Z

tests/.nftignore

 star_rsem/*.{genes,isoforms}.results
 star_rsem/log/*.log
-star_salmon/log/*.Log.{final.out,out,progress.out}
+star_{salmon,rsem}/log/*.Log.{final.out,out,progress.out}


Suggested change

star_{salmon,rsem}/log/*.Log.{final.out,out,progress.out}

star_{rsem,salmon}/log/*.Log.{final.out,out,progress.out}

obvious nitpick

I'll see if there's other feedback before I trigger the ci just for that ;-)

maxulysse

I had to wrap my head around the changes from RSEM since I didn't follow the PR that was changing that, but all good to me

JoseEspinosa

Just a small suggestion regarding the changelog, otherwise LGTM 🚀

CHANGELOG.md

maxulysse and others added 30 commits August 18, 2025 10:18

back to dev

5bbcc07

Merge pull request #1597 from nf-core/back_to_dev

072dbcc

Bump version back to dev after release 3.20.0

First pass allow bam input

346e42a

Add samplesheet output with bams

83e312f

Fix up bam samplesheet generation

fac2cee

Misc fixes

fd2d5ee

Fix alignment

6e32ed7

Remove view

b0c3d10

Rework percent mapping usage to allow for bam input

627fa9c

Fix ID issue

68ea671

Fix mapping rate to samplesheet

a1eb7a1

Linting fixes

a172f46

Strip trailing whitespace

6748397

Correct function tests for function changes

0e3d4ac

Fix percent mapped handling

662cca5

Fix usage formatting for pre-commit

fca5dfd

Skipping alignment no longer necessarily means skipping bam processing

51d9ca5

Don't output failed mappings with null mapping rate

776d903

More config fixes now we might be post-processing bams after we skip …

346178e

…alignment

Add not on bam reprocessing

13749c7

pre-commit fix

235589e

update snap

ccbf323

Bump multiqc

1a3175e

Add bam input test

89ddb3c

RO-crate fix

ce1327a

Update test exclusions

9b07d79

Merge branch 'bam_entry_point' of github.com:nf-core/rnaseq into bam_…

544a4de

…entry_point

Try some manual snapshot fixes

efd6236

Merge branch 'bam_entry_point' of github.com:nf-core/rnaseq into bam_…

3f34c9a

…entry_point

Improve docs

e16b8dc

pinin4fjords added 25 commits September 15, 2025 16:24

Remove commented rsem index

e5add62

Update rsem subworkflow test, stripping hard-to-test sentieon test

fc0686f

Bump rsem sentieon module

d50bb9b

Readd versions from rsem swf

9f40616

Update rsem snaps

f9cd5cd

Delete pipeline star_rsem sention tests

8d27efc

Update bam input snap

4a97a75

Don't need to publish bam files from RSEM

450cc33

RSEM now needs an index even without alignment

68488c5

Fix bam input test for rsem

a467b3d

Add target quantifier warning

1f983cb

Don't snapshot star logs now for rsem

0d2764d

Fix star_rsem snap for log exclusion

fd6de75

Update changelog

e6f1cc0

Prettier

d35b674

Remove old alignment assertions from rsem test

818d79d

Tweak to only use BAM files with --skip_alignment

91d7d26

Merge pull request #1604 from nf-core/rsem_bam_input

00a0a15

Enable BAM input for RSEM

Fix default for umi_discard_read to prevent validation errors in Plat…

ead60fd

…form

Update changelog

ef4c511

Merge pull request #1605 from nf-core/fix_umi_discard_default

c003e2d

Fix default for umi_discard_read to prevent validation errors in Platform

Bump versions for 3.21.

6aa18da

update changelog

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Prettier

722bb47

Merge pull request #1606 from nf-core/pre_3.21.0_bumps

13c6e21

Bump version to 3.21.0 ahead of release

maxulysse reviewed Sep 18, 2025

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maxulysse approved these changes Sep 18, 2025

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JoseEspinosa approved these changes Sep 18, 2025

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pinin4fjords merged commit 9738a2d into master Sep 18, 2025
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Dev -> Master for 3.21.0 #1607

Dev -> Master for 3.21.0 #1607

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pinin4fjords commented Sep 18, 2025 •

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	star_{salmon,rsem}/log/*.Log.{final.out,out,progress.out}
	star_{rsem,salmon}/log/*.Log.{final.out,out,progress.out}

Dev -> Master for 3.21.0 #1607

Dev -> Master for 3.21.0 #1607

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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pinin4fjords commented Sep 18, 2025 •

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