refactor preprocessing, one more time #494
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…better_faster_stronger
maxulysse
changed the title
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reverted gatk4 spark containers to a version that was actually working |
😢 I don't get why it doesn't work with the new one. Doesn't look like the base containers is changing. but great that you fixed it 🚀 |
I'm as confused as you are |
| @@ -244,14 +244,12 @@ process { | |||
| withName: "BWA.*MEM" { | |||
| ext.args = { meta.status == 1 ? '-K 100000000 -M -B 3' : '-K 100000000 -M' } | |||
| ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.findAll(/part_([0-9]+)?/).last()) : "" } | |||
| publishDir = [ | |||
| enabled: false | |||
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Isn't this the default? I think we discuss this in one of the previous PR'S?
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Wasn't working properly actually
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oh ok, so should be added back then to the other modules? Or is only BWA not working?
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no idea, I'll need to do some more proper tests with that
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oh, good point, I'll check this out
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still not, I have no idea why I have the bam if I don't have this enabled: false here
PR checklist
scrape_software_versions.pynf-core lint .).nextflow run . -profile test,docker).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).