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add saltshaker modules #775

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ieduba wants to merge 35 commits intodevfrom
saltshaker
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add saltshaker modules #775
ieduba wants to merge 35 commits intodevfrom
saltshaker

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@ieduba ieduba commented Feb 24, 2026

PR checklist

  • 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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_singleton,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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nf-core-bot commented Feb 24, 2026

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
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.

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github-actions bot commented Feb 24, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 493a43a

+| ✅ 244 tests passed       |+
#| ❔   7 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗   8 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ mq_metrics = SENTIEON_DATAMETRICS.out.mq_metrics.ifEmpty(null) // channel: [ val(meta), path(mq_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ qd_metrics = SENTIEON_DATAMETRICS.out.qd_metrics.ifEmpty(null) // channel: [ val(meta), path(qd_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_metrics = SENTIEON_DATAMETRICS.out.gc_metrics.ifEmpty(null) // channel: [ val(meta), path(gc_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ gc_summary = SENTIEON_DATAMETRICS.out.gc_summary.ifEmpty(null) // channel: [ val(meta), path(gc_summary) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ aln_metrics = SENTIEON_DATAMETRICS.out.aln_metrics.ifEmpty(null) // channel: [ val(meta), path(aln_metrics) ]
    _
  • pipeline_if_empty_null - ifEmpty(null) found in /home/runner/work/raredisease/raredisease/subworkflows/local/align_sentieon/main.nf: _ is_metrics = SENTIEON_DATAMETRICS.out.is_metrics.ifEmpty(null) // channel: [ val(meta), path(is_metrics) ]
    _
  • schema_lint - Input mimetype is missing or empty
  • schema_description - No description provided in schema for parameter: hisat2

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • modules_config - modules_config

❔ Tests fixed:

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-03-20 13:47:02

@ieduba ieduba changed the title add saltshaker modules and run mitosalt from bin add saltshaker modules Feb 24, 2026
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ieduba commented Feb 26, 2026

@nf-core-bot fix linting

@ieduba ieduba marked this pull request as ready for review February 27, 2026 10:13
sofiademmou
sofiademmou reviewed Mar 2, 2026
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Great job ! :)
We put some comments on saltshaker_call that can apply to classify and plot as well.
Do you need to update the CHANGELOG.md, README, and documentation (output and usage) maybe ?

modules/local/mitosalt/resources/usr/bin/MitoSAlt1.1.1.pl
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@sofiademmou sofiademmou Mar 2, 2026

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Do you think this should be in the templates directory ? https://nf-co.re/docs/guidelines/components/modules#module-template-location

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@ieduba ieduba Mar 4, 2026

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nextflow docs say that templates are discouraged and should only be used for bash scripts (https://www.nextflow.io/docs/latest/process.html#template) which is why I went with the bin. We can discuss more and see what nf-core folks think when/if this becomes an nf-core module

modules/nf-core/saltshaker/call/main.nf
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@sofiademmou sofiademmou Mar 2, 2026

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Could this be an nf-core module ? And have tests ?

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@ieduba ieduba Mar 4, 2026

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Yes! will do :)

subworkflows/local/call_sv_MT/main.nf
.set{ch_saltshaker_in}

if (ch_saltshaker_in) {
SALTSHAKER_CALL(
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@sofiademmou sofiademmou Mar 2, 2026

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What happens if there is no files left after the filtering ?

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@ieduba ieduba Mar 3, 2026

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saltshaker is then skipped, because it only makes sense to run it if there are calls from mitosalt (also saltshaker crashes otherwise)

tests/default.nf.test.snap
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@sofiademmou sofiademmou Mar 2, 2026

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I don't see any output files for saltshaker ?

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@ieduba ieduba Mar 3, 2026

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saltshaker was being skipped in testing because the test output file for mitosalt was empty. fixed by adding a line of text to that file in stub

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jemten commented Mar 2, 2026

Could you add a citation reference for mitosalt and saltshaker as well

@ieduba
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ieduba commented Mar 4, 2026

@nf-core-bot fix linting

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