Merge branch `Dev` into `fusioninspector_workflow` #3

delfiterradas · 2025-08-29T13:48:45Z

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
If necessary, also make a PR on the nf-core/rnafusion branch on the nf-core/test-datasets repository.
Make sure your code lints (nf-core lint).

Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

…me functionality

…tools

Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com>

…-core

Change to nf-core subworkflow of `fastq_align_star`

github-actions · 2025-08-29T13:52:19Z

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

Posted for pipeline commit acdf635

+| ✅ 302 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   9 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
pipeline_todos - TODO string in nextflow.config: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0
pipeline_if_empty_null - ifEmpty(null) found in main.nf: _ stringtie_gtf = ch_stringtie_gtf.ifEmpty(null) // channel: [meta, gtf]
_
schema_lint - Input mimetype is missing or empty
schema_description - No description provided in schema for parameter: save_trimmed_fail
schema_description - No description provided in schema for parameter: min_trimmed_reads
schema_description - No description provided in schema for parameter: save_merged

❔ Tests ignored:

files_exist - File is ignored: tests/default.nf.test
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

✅ 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-rnafusion_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-rnafusion_logo_light.png
files_exist - File found: docs/images/nf-core-rnafusion_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: main.nf
files_exist - File found: assets/multiqc_config.yml
files_exist - File found: conf/base.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-rnafusion_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/WorkflowRnafusion.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 ends in dev: 4.0.0dev
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.read_length= 100
nextflow_config - Config default value correct: params.fusioncatcher_limitSjdbInsertNsj= 2000000
nextflow_config - Config default value correct: params.fusioninspector_limitSjdbInsertNsj= 1000000
nextflow_config - Config default value correct: params.ctatsplicing_cancer_introns= https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/CANCER_SPLICING_LIB_SUPPLEMENT/cancer_introns.GRCh38.Jun232020.tsv.gz
nextflow_config - Config default value correct: params.annot_filter_url= https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm
nextflow_config - Config default value correct: params.tools_cutoff= 1
nextflow_config - Config default value correct: params.min_trimmed_reads= 1
nextflow_config - Config default value correct: params.species= homo_sapiens
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/test_build.nf.test' contains outdir parameter
nf_test_content - 'tests/test_build.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_build.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.nf.test' contains outdir parameter
nf_test_content - 'tests/test_stub_bam.nf.test' snapshots a 'versions.yml' file
nf_test_content - 'tests/test_stub_bam.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 - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
nf_test_content - 'tests/nextflow.config' contains pipelines_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 - assets/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_light.png matches the template
files_unchanged - docs/images/nf-core-rnafusion_logo_dark.png 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 Nextflow minimum version badge matched config. Badge: 24.10.5, Config: 24.10.5
readme - README nf-core template version badge 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_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: 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: 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
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 subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
base_config - conf/base.config found and not ignored.
modules_config - conf/modules.config found and not ignored.
modules_config - ARRIBA_ARRIBA found in conf/modules.config and Nextflow scripts.
modules_config - ARRIBA_VISUALISATION found in conf/modules.config and Nextflow scripts.
modules_config - BIOAWK found in conf/modules.config and Nextflow scripts.
modules_config - CTATSPLICING_STARTOCANCERINTRONS found in conf/modules.config and Nextflow scripts.
modules_config - GENCODE_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FASTP_FOR_FUSIONCATCHER found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_RAW found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_TRIM found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONCATCHER_FUSIONCATCHER found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONINSPECTOR found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONREPORT_DETECT found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONREPORT_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_BEDTOINTERVALLIST found in conf/modules.config and Nextflow scripts.
modules_config - GATK4_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
modules_config - GFFREAD found in conf/modules.config and Nextflow scripts.
modules_config - GTF_TO_REFFLAT found in conf/modules.config and Nextflow scripts.
modules_config - HGNC_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTINSERTSIZEMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - PICARD_COLLECTRNASEQMETRICS found in conf/modules.config and Nextflow scripts.
modules_config - SALMON_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SALMON_QUANT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_CONVERT found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_SORT found in conf/modules.config and Nextflow scripts.
modules_config - STAR_ALIGN found in conf/modules.config and Nextflow scripts.
modules_config - STAR_GENOMEGENERATE found in conf/modules.config and Nextflow scripts.
modules_config - STARFUSION_BUILD found in conf/modules.config and Nextflow scripts.
modules_config - CTATSPLICING_PREPGENOMELIB found in conf/modules.config and Nextflow scripts.
modules_config - STRINGTIE_MERGE 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: 3.3.2
rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

nf-core/tools version 3.3.2
Run at 2025-08-29 13:52:01

atrigila and others added 25 commits August 21, 2025 19:26

refact: replace local trim_workflow for nf-core subworkflow with sa…

5a38668

…me functionality

fix: replace for new module names in config

0d0c739

test: update snapshot

fcbf9db

style: improve ifempty usage

5560282

chore: remove unused parameters, add new trim params

82dbc7c

chore: remove unused file

cc302d6

docs: update changelog

889c219

chore: remove non-existent test

6057891

Change to nf-core subworkflow of fastq_align_star

f8a5790

Add emits to fastq_align_star subworkflow

baf957e

Update stub test

859edab

Patch subworkflows to avoid lint failures

5071899

Update santools/sort and keep original subworkflow bam_sort_stats_sam…

8282dc0

…tools

Update nextflow.config

9c560e8

Update stub test snapshot

e3e4c13

Replace modules in test for QC_WORKFLOW

8a9d157

Update workflows/rnafusion.nf

225aeb9

Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com>

Update CHANGELOG.md

c59cd57

test: update snapshot

66077fb

Merge pull request nf-core#752 from atrigila/replace_trim_sbwf_for_nf…

f9247cd

…-core

Merge branch 'dev' into fastq_align_star

fc66372

Fix modules.json

b8e59d4

Fix main.nf.test.snap

5e0383b

Merge pull request nf-core#756 from delfiterradas/fastq_align_star

82042b4

Change to nf-core subworkflow of `fastq_align_star`

Merge branch 'fusioninspector_workflow' into dev

acdf635

delfiterradas closed this Aug 29, 2025

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Merge branch `Dev` into `fusioninspector_workflow` #3

Merge branch `Dev` into `fusioninspector_workflow` #3

Uh oh!

delfiterradas commented Aug 29, 2025

Uh oh!

github-actions bot commented Aug 29, 2025

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Merge branch Dev into fusioninspector_workflow #3

Merge branch Dev into fusioninspector_workflow #3

Uh oh!

Conversation

delfiterradas commented Aug 29, 2025

PR checklist

Uh oh!

github-actions bot commented Aug 29, 2025

nf-core pipelines lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Merge branch `Dev` into `fusioninspector_workflow` #3

Merge branch `Dev` into `fusioninspector_workflow` #3

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