Add --aligner #283
Add --aligner #283
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both commands work: and |
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Sorry for the huge PR. |
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Is the documentation a copy from dev ? (except for bwamem2) |
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I checked-out most of the files from |
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| #### GATK MarkDuplicatesSpark | ||
| Such files are intermediate and not kept in the final files delivered to users. |
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It is a bit unclear for me here, which files are not delivered to the user. The mapped bams? Similar in the BWA section
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Yes, especially since they're not merged.
But yeah, not very clear
| bam_bwamem2 = BWAMEM2_MEM.out | ||
| } | ||
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| bam_bwamem2 = bam_bwamem2.mix(bwa_mem_out) |
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I think we should use just bam_bwa or something. If bwamem2 was not used for mapping, the channel will still be called that for the remainder of the pipeline
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Or will this not work because of empty channels or what not?I suppose we can also work on naming as we go, since all the things are changing so much still
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| /* | |||
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These are the functions from the modules repo right? We should probably find a common place for them, otherwise we will have them x-times in the end (if that works)
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Actually just used nf-core modules install . bwa/index
Maybe it's something that need to be fixed within the nf-core/modules repo
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ok, maybe this can be discussed in the modules channel. Could be tricky to figure out during the installation whether another module has been installed and thus the functions are there.
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If it's always the same functions, then it can be in a specific path within the modules folder.
Should be easy to check if it exists
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I guess for now, here we can leave it as is
ok, I have not read about everything in the docu now. Focused on the changes for the aligner. Skimmed only over the rest |
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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