Add subworkflow for gridss somatic structural variant calling - #12574
Open
imsarath wants to merge 7 commits into
Open
Add subworkflow for gridss somatic structural variant calling#12574imsarath wants to merge 7 commits into
imsarath wants to merge 7 commits into
Conversation
SPPearce
reviewed
Aug 18, 2026
SPPearce
reviewed
Aug 19, 2026
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = channel.of([ |
Contributor
There was a problem hiding this comment.
Shouldn't need the channel.of or channel.value at all.
Contributor
Author
There was a problem hiding this comment.
I tried removing it completely, but input[0] and input[1] still require it.
| ch_fasta_fai_bwaindex // channel: [ val(meta2), fasta, fai, bwa_index ] | ||
| ch_pondir // channel: [ val(meta3), [ pondir ] ] | ||
| ch_gridss_config // channel: [ val(meta4), [ gridss_config ] ] | ||
| val_target_bed // string: target BED for panel/exome data, null to run untargeted |
Contributor
Author
There was a problem hiding this comment.
Yes, it's a groovy path value for target_bed. I realized we could implement this in a cleaner way, so I've updated the code a bit. Let me know what you think of this approach!
SPPearce
reviewed
Aug 19, 2026
SPPearce
left a comment
SPPearce
left a comment
Contributor
There was a problem hiding this comment.
Can you format the main.nf with each module argument on its own line too please
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
This PR adds
bam_tumor_normal_somatic_structural_variant_calling_gridss, a subworkflow that calls somatic structural variants from a tumor/normal BAM pair. It chains the full GRIDSS workflow - optional targeted fragment extraction, per-sample preprocess, joint assembly and call, thengridss_somatic_filter. It emits the unfiltered joint VCF plus the all-somatic and high-confidence somatic call sets.PR checklist
Closes #4498
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