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Feature/gene fusion - #52

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Jorisvansteenbrugge merged 33 commits into
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feature/gene_fusion
Mar 6, 2026
Merged

Feature/gene fusion#52
Jorisvansteenbrugge merged 33 commits into
developfrom
feature/gene_fusion

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@Jorisvansteenbrugge

@Jorisvansteenbrugge Jorisvansteenbrugge commented Feb 9, 2026

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This PR adds:

  • A new subworkflow to detect gene fusion events by combining two tools (starfusion and arriba) and generating a combined report using fusionreport
    • Including a unit-test
  • When a sample is sequenced on multiple lanes, alignment using STAR_ALIGN is now done on fastq files of all lanes together --> This is necessary for starfusion. Previously this was done by mapping lanes individually and then merging the resulting bam files.
    • Including a unit-test
  • UMITOOLS dedup workflow is now optional, but enabled by default, to make the pipeline more universally applicable.
  • A minimum on the requested run time and memory for SLURM jobs is now included to avoid requesting 1 minute/1mb SLURM jobs that timeout/get killed

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Jorisvansteenbrugge marked this pull request as draft February 9, 2026 09:16
@Jorisvansteenbrugge
Jorisvansteenbrugge marked this pull request as ready for review February 9, 2026 09:52
@ALuesink
ALuesink self-requested a review February 27, 2026 12:04

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LGTM, just some small comments.

Comment thread conf/modules.config Outdated
Comment thread conf/modules.config Outdated
Comment thread conf/modules.config Outdated
Comment thread subworkflows/local/fastq_trim_filter_align_dedup/tests/main.nf.test

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All comments have been addressed

@Jorisvansteenbrugge
Jorisvansteenbrugge merged commit 2d2e282 into develop Mar 6, 2026
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@Jorisvansteenbrugge
Jorisvansteenbrugge deleted the feature/gene_fusion branch March 6, 2026 13:16
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2 participants