Important! Template update for nf-core/tools v3.3.2 by nf-core-bot · Pull Request #702 · nf-core/rnafusion

nf-core-bot · 2025-07-08T11:40:21Z

Version 3.3.2 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.2 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.2 release page.

github-actions · 2025-07-14T13:11:30Z

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

Posted for pipeline commit 2203644

+| ✅ 297 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

Details

❗ Test warnings:

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
local_component_structure - fusioninspector_workflow.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ 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: 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-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.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_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_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_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 - '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: fix_linting.yml
actions_schema_validation - Workflow validation passed: clean-up.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: awstest.yml
actions_schema_validation - Workflow validation passed: linting.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: awsfulltest.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: branch.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 modules directory structure is correct 'modules/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_DOWNLOAD found in conf/modules.config and Nextflow scripts.
modules_config - ARRIBA_VISUALISATION 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 found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC_FOR_FASTP found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONCATCHER_FUSIONCATCHER found in conf/modules.config and Nextflow scripts.
modules_config - FUSIONCATCHER_DOWNLOAD 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 - 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 2025-07-28 13:01:51

…core/rnafusion into nf-core-template-merge-3.3.2

nf-core-bot added 2 commits June 3, 2025 11:02

Template update for nf-core/tools version 3.3.1

3710466

Template update for nf-core/tools version 3.3.2

f387154

nf-core-bot mentioned this pull request Jul 8, 2025

Important! Template update for nf-core/tools v3.3.1 #675

Closed

rannick added 2 commits July 14, 2025 13:22

fix merge conflicts

0d00920

update for nf-lint

6a2d669

rannick added 24 commits July 14, 2025 15:13

Merge branch 'dev' into nf-core-template-merge-3.3.2

245b43e

linting

99d0d41

Merge branch 'nf-core-template-merge-3.3.2' of https://github.com/nf-…

916dd22

…core/rnafusion into nf-core-template-merge-3.3.2

end-of-file

4d2a71c

update hgnc

ff88e3e

update fusionreport

e86c41b

update snaps

b76c8bb

update tests

07ca9cf

remove starfusion workflow (will be moved to modules)

0498949

Merge branch 'dev' into nf-core-template-merge-3.3.2

41f0558

re-upload arriba

945b3a5

udpate

61666aa

update fusioncatcher download

4c1269d

update ctatsplicing snap

b5da338

update arriba vis snap

e6519af

update fusioncatcher download link

5385242

update fusioncatcher download link pattern check

233bc0e

auto confirm

d53f43a

update stringtie workflow

a909212

update version stringtie snap

b4b2cff

remove cosmic test

e5dda65

update tests

5ea8679

update link and download process

bb8a1df

add fuzzy option

7703d6a

rannick requested a review from atrigila as a code owner July 18, 2025 13:22

rannick added 11 commits July 18, 2025 15:23

Merge branch 'dev' into nf-core-template-merge-3.3.2

09b2bd2

update qc_workflow snap

55c621c

update hgnc snap

5b696f2

update snap

dea24e6

update snaps

000f3a3

update snap

4baff3a

update snap

a03df57

Merge branch 'nf-core-template-merge-3.3.2' of https://github.com/nf-…

9f64683

…core/rnafusion into nf-core-template-merge-3.3.2

update rocrate

0236e29

update snap

f2b9c5d

update fusioninspector snap

e377261

This was referenced Jul 23, 2025

refact: remove unused subworkflows #723

Merged

Add S3 references to the pipeline #717

Merged

rannick added 13 commits July 23, 2025 14:58

update snap

86fddeb

update test to exclude exact match for files with dates

118d1ba

Merge branch 'dev' into nf-core-template-merge-3.3.2

3108533

Merge branch 'nf-core-template-merge-3.3.2' of https://github.com/nf-…

94658fd

…core/rnafusion into nf-core-template-merge-3.3.2

update input to STARFUSION BUILD

426bb51

update prettier

1a6c91e

update ctat test

7fe1607

prettier

29185bd

update ctat test

9d3fb7e

update starfusion detect test

de664dc

update fusioninspector

7efcefe

update fusioninspector test

3613777

update fusioncatcher test

2203644

rannick approved these changes Jul 29, 2025

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rannick merged commit c9b73a6 into dev Jul 29, 2025
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rannick deleted the nf-core-template-merge-3.3.2 branch July 29, 2025 09:26

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Important! Template update for nf-core/tools v3.3.2#702

Important! Template update for nf-core/tools v3.3.2#702
rannick merged 61 commits intodevfrom
nf-core-template-merge-3.3.2

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nf-core-bot commented Jul 8, 2025

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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