8000 Run CRAM_TO_BAM only once per pipeline run · Issue #1830 · nf-core/sarek · GitHub
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Run CRAM_TO_BAM only once per pipeline run #1830

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famosab opened this issue Mar 12, 2025 · 1 comment
A536
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Run CRAM_TO_BAM only once per pipeline run #1830

famosab opened this issue Mar 12, 2025 · 1 comment
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enhancement New feature or request

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@famosab
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famosab commented Mar 12, 2025

Description of feature

At the moment multiple modules do not work with cram files (cnvkit, muse, lofreq). We opened issues to ask the maintainers of these tools to add that functionality. In the meantime this should be handled in a way that does not re-run the conversion multiple times when multiple callers are used. My proposal would be

  • before doing any variant calling check if tools where chosen that need bam files
  • change the other code to then keep outputting bams alongside the crams and feed the bams to those tools
@famosab famosab added the enhancement New feature or request label Mar 12, 2025
@FriederikeHanssen
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Not sure is BQSR can output both, although that would be neat. Markdup should be able to.
Otherwise we could at least centralise the conversion step

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@FriederikeHanssen @famosab
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