Release PR 4.1.0 by nvnieuwk · Pull Request #789 · nf-core/rnafusion

nvnieuwk · 2026-02-09T10:05:49Z

Added

Added a BAM/CRAM conversion to FASTQ step to run tools that depend on FASTQ files. It still is advised to supply a FASTQ file if possible to reduce runtime of the pipeline. #783

Fixed

Fix issue with vcf_collect when no fusions are found by fusioninspector #786

See https://nfcore.slack.com/archives/C050DNB6K5H/p1762184179238379 for details

Add a bam/cram to fastq conversion step

Fix vcf-collect filter when fusions are missing from fusioninspector

Bump to 4.1.0

nf-core-bot · 2026-02-09T10:06:28Z

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.3.2.
Please update your pipeline to the latest version.

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

github-actions · 2026-02-09T10:08:42Z

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

Posted for pipeline commit e9b58b9

+| ✅ 312 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   3 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: conf/igenomes.config
files_exist - File not found: conf/igenomes_ignored.config
included_configs - Pipeline config does not include custom configs. Please add the includeConfig line.

❔ 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 does not contain dev for release: 4.1.0
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.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_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/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.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: template-version-comment.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: fix_linting.yml
actions_schema_validation - Workflow validation passed: nf-test.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: clean-up.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 - AGAT_CONVERTGFF2BED found in conf/modules.config and Nextflow scripts.
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.
version_consistency - Version tags are consistent: manifest.version = 4.1.0, nfcore_yml.version = 4.1.0

Run details

nf-core/tools version 3.3.2
Run at 2026-02-10 08:35:18

Fix a typo in awsfulltests

mashehu and others added 21 commits November 3, 2025 16:44

Update to new runner size syntax

05cc0ec

See https://nfcore.slack.com/archives/C050DNB6K5H/p1762184179238379 for details

Merge pull request #779 from nf-core/mashehu-patch-1

3607f8f

add a bam conversion step

5521e3b

fix wrong fusioncatcher output, fix tests, add test

2b7c218

address comments

1906acb

pre-commit

8f6885f

Apply suggestions from code review

cc064fb

Merge pull request #783 from nvnieuwk/bam-conversion

4576d21

Add a bam/cram to fastq conversion step

fix vcf-collect filter when fusions are missing from fusioninspector

5cd5acd

Merge branch 'dev' into fix/vcf-collect

6059451

also adjust PosB check

e541c0a

changelog

917cee8

check if orig_* is na

ca8a302

fix test

e9bc2fc

fix missing chromosome issues

8c49ee2

move positional filter right before VCF creation

a4164d2

Merge pull request #786 from nvnieuwk/fix/vcf-collect

9239657

Fix vcf-collect filter when fusions are missing from fusioninspector

bump to 4.1.0

c5cb928

update snaps

ff31261

add zenodo doi

5fd8c87

Merge pull request #788 from nvnieuwk/bump/4.1.0

ccbf55d

Bump to 4.1.0

nvnieuwk requested review from atrigila and rannick as code owners February 9, 2026 10:05

maxulysse approved these changes Feb 9, 2026

View reviewed changes

nvnieuwk and others added 2 commits February 10, 2026 09:29

fix a typo in awsfulltests

be7df15

Merge pull request #790 from nvnieuwk/fix/awsfulltests

e9b58b9

Fix a typo in awsfulltests

apeltzer approved these changes Feb 10, 2026

View reviewed changes

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Release PR 4.1.0#789

Release PR 4.1.0#789
nvnieuwk wants to merge 23 commits intomasterfrom
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nvnieuwk commented Feb 9, 2026

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github-actions bot commented Feb 9, 2026 •

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nvnieuwk commented Feb 9, 2026

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nf-core-bot commented Feb 9, 2026

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nf-core pipelines lint overall result: Passed ✅ ⚠️

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github-actions bot commented Feb 9, 2026 •

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