Fix behavior when no fusion is present by rannick · Pull Request #714 · nf-core/rnafusion

rannick · 2025-07-16T07:56:27Z

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).

github-actions · 2025-07-16T07:56:35Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
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 · 2025-07-16T07:57:45Z

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

Posted for pipeline commit 2c710b6

+| ✅ 307 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config

❔ 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.
readme - README Zenodo placeholder was replaced with DOI.
pipeline_todos - No TODO strings found
pipeline_if_empty_null - No ifEmpty(null) strings 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_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: 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_CREATESEQUENCEDICTIONARY 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 - UCSC_GTFTOGENEPRED 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 2025-09-09 12:47:50

rannick · 2025-07-17T13:25:09Z

Waiting for test to finish

…o no_fusions

…nwards analysis is still triggered

subworkflows/local/fusioninspector_workflow.nf

nvnieuwk

Two small comments, why did you delete the test snapshot though?

subworkflows/local/fusioninspector_workflow/main.nf

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

…o no_fusions

nvnieuwk

LGTM, thanks!

rannick added 2 commits July 15, 2025 13:50

handle no fusion cases

b3bbb79

update fusioninspector

034876f

rannick marked this pull request as ready for review July 16, 2025 08:06

rannick marked this pull request as draft July 16, 2025 08:06

rannick added 2 commits July 16, 2025 12:27

update logical gate and snap fusioninsp

94eacdb

update tests

5a0ee3a

rannick changed the base branch from master to dev July 16, 2025 12:10

rannick added 2 commits July 16, 2025 16:21

Merge branch 'dev' into no_fusions

8388616

Merge branch 'dev' into no_fusions

44b7823

rannick self-assigned this Jul 17, 2025

rannick added 4 commits July 17, 2025 13:38

update arriba refs params

ae357ec

update changelog

de2541e

update schema

43a8ebd

Merge branch 'dev' into no_fusions

ebb0183

rannick added 13 commits July 25, 2025 10:35

Merge branch 'dev' into no_fusions

f9fa7c2

change logic

2196478

Merge branch 'no_fusions' of https://github.com/nf-core/rnafusion int…

be81566

…o no_fusions

udpate logic

a3843ee

Merge branch 'dev' into no_fusions

52f37b1

Merge branch 'dev' into no_fusions

4a25a22

fix issues and add characters to fusioninspectore stub run so the dow…

71fc45f

…nwards analysis is still triggered

update snape

ed7d88d

intermetiate snap update

8205a98

dev merge

d6e80c9

update snap

766b0f8

update snap

cf5802e

update qc workflow test and snap

605cbc7

nvnieuwk reviewed Sep 1, 2025

View reviewed changes

subworkflows/local/fusioninspector_workflow.nf Outdated Show resolved Hide resolved

nvnieuwk reviewed Sep 1, 2025

View reviewed changes

subworkflows/local/fusioninspector_workflow.nf Show resolved Hide resolved

rannick added 2 commits September 1, 2025 15:03

fix merge conflicts and use branching instead of if statements

21e21b1

reshuffling

a347208

nvnieuwk reviewed Sep 1, 2025

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rannick and others added 7 commits September 2, 2025 10:27

Update subworkflows/local/fusioninspector_workflow/main.nf

59fcd54

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

Update subworkflows/local/fusioninspector_workflow/main.nf

08c7dec

Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com>

update

36221f8

remove zombie line

d2a4764

update snap

e765480

udpate snap bam

9dddc25

change operator

e7c12b0

rannick mentioned this pull request Sep 3, 2025

vcf output is not created if no fusions are found #673

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rannick added 7 commits September 3, 2025 13:33

Merge branch 'dev' into no_fusions

aa2b30c

update snaps

9931490

Merge branch 'dev' into no_fusions

d8dd843

fix fusioninspector workflow

73113eb

Merge branch 'no_fusions' of https://github.com/nf-core/rnafusion int…

1141d24

…o no_fusions

update build snap

bd3fddc

qc test fixes

82608dd

rannick marked this pull request as ready for review September 9, 2025 12:37

rannick requested a review from atrigila as a code owner September 9, 2025 12:37

Merge branch 'dev' into no_fusions

2c710b6

nvnieuwk approved these changes Sep 9, 2025

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rannick merged commit b1c222c into dev Sep 9, 2025
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rannick deleted the no_fusions branch September 9, 2025 13:42

atrigila mentioned this pull request Sep 16, 2025

Release 4.0.0 #766

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Fix behavior when no fusion is present#714

Fix behavior when no fusion is present#714
rannick merged 40 commits intodevfrom
no_fusions

rannick commented Jul 16, 2025

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❗ Test warnings:

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rannick commented Jul 17, 2025

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rannick commented Jul 16, 2025

PR checklist

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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