Add a new module - gridss/extractoverlappingfragments - #12450
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imsarath
marked this pull request as draft
July 28, 2026 12:19
SPPearce
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Jul 29, 2026
| output: | ||
| tuple val(meta), path("*.subset.bam"), emit: bam | ||
| tuple val("${task.process}"), val('gridss'), eval("CallVariants --version 2>&1 | sed 's/-gridss//'"), topic: versions, emit: versions_gridss | ||
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Please add the disambiguation check to ensure that the input and output bams don't have the same name.
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Yes, sure. Added the disambiguation check. Thanks for the review 👍
imsarath
marked this pull request as ready for review
July 29, 2026 13:38
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
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This PR adds a module for gridss/extractoverlappingfragments; It extracts all alignments for read pairs with at least one alignment overlapping a set of regions of interest (including mate reads and supplementary alignments). This script is part of the GRIDSS toolkit and is primarily used to extract reads of interest for targeted GRIDSS structural variant calling. Github - PapenfussLab/gridss; The script is bundled within the main gridss installation
PR checklist
Closes #12422
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda