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Allow on restart to not convert the bam files to cram #1162

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YussAb opened this issue Jul 24, 2023 · 0 comments
Closed

Allow on restart to not convert the bam files to cram #1162

YussAb opened this issue Jul 24, 2023 · 0 comments
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enhancement New feature or request

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@YussAb
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YussAb commented Jul 24, 2023

Description of feature

Dear nf-core community, thank you very much for your incredible work!

I'm working with WGS samples with 100 X coverage. I have bam and bai files.
When I run sarek on these files I have to wait from 4 to 6 hour to convert them from bam to cram and I don't even need those cram files.
I was wondering if it could be possible to create and option to work exclusively with bam instead of cram.

Furthermore, looking at the code and modules, I found that BAM_MARKDUPLICATES:GATK4_MARKDUPLICATES is the main gateway to cram instead of bam outputs.

https://github.com/nf-core/sarek/blob/3.1.2/modules/nf-core/gatk4/markduplicates/main.nf

Probably with a slight modification to this modules, making it optional to convert from bam to cram after markduplicates, it'll also be possible to have bam outputs without converting cram to bam when using the full pipeline starting from fastq inputs.

Thank you in advance and best regards!
Youssef
@YussAb YussAb added the enhancement New feature or request label Jul 24, 2023
@FriederikeHanssen FriederikeHanssen mentioned this issue Nov 8, 2024
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maxulysse added a commit that referenced this issue Nov 12, 2024
@FriederikeHanssen @maxulysse
Don't convert input bam files that are supplied in post-alignment ste…
79d749e 
…ps, it's not necessary. (#1728)

Thank you to @SPPearce for chatting with me again to finally remove this
wasteful step.

Closes #1162

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## PR checklist

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---------

Co-authored-by: Maxime U Garcia <[email protected]>
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@FriederikeHanssen @YussAb