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Add VCFtools #568
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Add VCFtools #568
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szilvajuhos
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Apr 16, 2018
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These is still mutect1 at many places, but I guess these are going to disappear with #567
| @@ -211,8 +212,8 @@ def helpMessage() { | |||
| log.info " Default: all" | |||
| log.info " Possible values:" | |||
| log.info " all, fastqc, freebayes, gatk, igvtools, multiqc, mutect1" | |||
| log.info " picard, qualimap, r-base, runallelecount, sarek" | |||
| log.info " snpeff, snpeffgrch37, snpeffgrch38, vepgrch37, vepgrch38" | |||
| log.info " picard, qualimap, r-base, runallelecount, sarek, snpeff" | |||
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We have fastqc, multiqc, qualimap, vcftools, as separate containers: these are all QC tools, is it possible to keep them separate, or can we merge these containers sometime?
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That could be a good idea, I'll think about it
| @@ -211,8 +212,8 @@ def helpMessage() { | |||
| log.info " Default: all" | |||
| log.info " Possible values:" | |||
| log.info " all, fastqc, freebayes, gatk, igvtools, multiqc, mutect1" | |||
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Should be mutect2 I guess
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No, mutect2 is shipped with the GATK container
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IC, of course. Shall I merge this first, or shall I wait for #567 ?
|
Yes, removing |
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close #368
vcftoolscontainerRunVcftoolsprocessConcatVCFprocess