Update modules once again#459
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maxulysse merged 22 commits intonf-core:devfrom Dec 2, 2021
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@drpatelh at first I was a big annoyed because I just had finally finished my refactoring of everything with the newest modules syntax a week ago, and I had to do it again with the newer newest syntax. I'm particularly proud of the rework of our local bwamem and bwamem2 modules that are now stripped of every sarek logic, and the rework it allowed for the mapping subworkflow. |
| // MAPPING | ||
| process { | ||
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| withName: "BWA.*MEM" { |
| // Only name sort if Spark for Markduplicates + duplicate marking is not skipped | ||
| if (('markduplicates' in params.use_gatk_spark) && (!params.skip_markduplicates)) { | ||
| process { | ||
| withName: "BWA.*_MEM" { ext.args2 = 'sort -n' } |
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This then overwrites the above config ext.args2 for BWAMEM?
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I'm hoping that we can also remove the part thingy from the bwa*mem processes
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I will think about how to do this. I am sure there is a way
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Where are you using it? I don't see it in the process anymore
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Oh yes, that's what I wanted to figure it out.
I'll let someone else try that, I'm going to the NGI retreat today, so won't be able to work much
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yep that is what I thought of, to also pull that in the modules config. I am glad I wasn't completely off here. I'll give it a try probably tomorrow afternoon
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plus by then maybe the yet new modules syntax is there and I can catch two birds with one stone 😆
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@FriederikeHanssen will you be adding the split_fastq logic in the bwamem modules in #462 or will you be doing that in a separate PR?
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I'll see that I can add it in :)
FriederikeHanssen
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From my side this looks all great. Taking the 'parameter logic' out of the subworkflow is pretty nice, makes the workflow look a lot simpler and less crowded. I can also now better see how we can make it work with UMI based subworkflow + mapping.
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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).