feat: samclip module #8999
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feat: samclip module #8999
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emmcauley
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SPPearce
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Sep 5, 2025
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This tool only works on sam files and only outputs sam tools?
I think this should be piped in and out of samtools inside the module.
Potentially also samtools fixmate to fix paired end reads.
…Seqera container, update tests
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Sep 15, 2025
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Other things to consider:
- I think it would be good to add args to the samtools commands, which would allow for e.g. sorting ready for tools that require name-sorted or template-coordinate sorted, or filtering via that first samtools view.
- Do we want to support making cram files?
- Do we want to support index creation inside the final samtools sort?
…decompressed reference if made
SPPearce
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Jan 8, 2026
SPPearce
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SPPearce
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Left comments for the versions.
Need to fix the meta as well.
SPPearce
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Jan 8, 2026
| { assert process.success }, | ||
| { assert snapshot( | ||
| process.out, | ||
| process.out.versions.collect{ path(it).yaml } |
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| process.out.versions.collect{ path(it).yaml } |
Co-authored-by: Simon Pearce <[email protected]>
SPPearce
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Jan 10, 2026
modules/nf-core/samclip/main.nf
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| if [ "${is_compressed}" = "true" ]; then | ||
| rm -f ${ref_filename} | ||
| fi | ||
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This PR adds a new module,
samclip, and corresponding tests.samclipis used to filter SAM files for soft and hard clipped alignments. Test data is derived from nf-coretest-datasets.PR checklist
Closes #8342
versions.ymlfile.labelnf-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