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Add new component: gridss/assemble#12382

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imsarath wants to merge 15 commits into
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imsarath:gridss_assemble
Open

Add new component: gridss/assemble#12382
imsarath wants to merge 15 commits into
nf-core:masterfrom
imsarath:gridss_assemble

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@imsarath

@imsarath imsarath commented Jul 17, 2026

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As a part of the distributed computing GRIDSS subworkflow #4498 , I added this gridss/assemble module. This module wraps the assemble step, which performs genome-wide break-end assembly: it takes the per-sample preprocessed data (along with the input BAM/BAI files and reference genome) and assembles the reads supporting candidate structural variants into a single .sv.assembly.bam. This assembly is the input required for the downstream variant-calling step

PR checklist

Closes #4502.

  • 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 module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@imsarath
imsarath marked this pull request as draft July 17, 2026 09:41
@imsarath
imsarath marked this pull request as ready for review July 24, 2026 08:56
@imsarath imsarath self-assigned this Jul 24, 2026
Comment thread modules/nf-core/gridss/assemble/main.nf Outdated
Comment thread modules/nf-core/gridss/assemble/main.nf Outdated
Comment thread modules/nf-core/gridss/assemble/main.nf Outdated
'quay.io/biocontainers/gridss:2.13.2--h50ea8bc_3' }"

input:
tuple val(meta), path(bams), path(bais), path(preprocess_dirs)

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Suggested change
tuple val(meta), path(bams), path(bais), path(preprocess_dirs)
tuple val(meta), path(bam), path(bai), path(preprocess_dir)

singular should be fine. use it also in the other instances

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Applied the suggestions, 👍

imsarath and others added 6 commits July 24, 2026 11:26
@imsarath
imsarath requested a review from mashehu July 24, 2026 13:37
@mashehu

mashehu commented Jul 24, 2026

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@nf-core-bot fix linting

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new module: gridss/assembly

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