Removing MuTect1 #567
Removing MuTect1 #567
Conversation
germlineVC.nf
Outdated
| @@ -402,12 +384,11 @@ process ConcatVCF { | |||
| set variantCaller, idPatient, idSampleNormal, idSampleTumor, file("*.vcf.gz") into vcfConcatenated | |||
| file("*.vcf.gz.tbi") into vcfConcatenatedTbi | |||
|
|
|||
| when: ( 'haplotypecaller' in tools || 'mutect1' in tools || 'mutect2' in tools || 'freebayes' in tools ) && !params.onlyQC | |||
| when: 'haplotypecaller' in tools && !params.onlyQC | |||
There was a problem hiding this comment.
I am a bit confused here, so it is germline calling, so all the somatic callers are removed, if I am correct.
There was a problem hiding this comment.
I remember now, germlineVC.nf definitively needs more cleaning.
Do you want me to do that in this PR, or in a separate one?
Like in the one that will fix the BQSR thingy
There was a problem hiding this comment.
Would be nice to keep it in a single PR (so we can backout :) ) There is no rush, we are going to use v2.0.0 for few weeks anyway.
germlineVC.nf
Outdated
| @@ -651,7 +632,6 @@ def defineDirectoryMap() { | |||
| 'haplotypecaller' : "${params.outDir}/VariantCalling/HaplotypeCaller", | |||
| 'gvcf-hc' : "${params.outDir}/VariantCalling/HaplotypeCallerGVCF", | |||
| 'manta' : "${params.outDir}/VariantCalling/Manta", | |||
| 'mutect1' : "${params.outDir}/VariantCalling/MuTect1", | |||
| 'mutect2' : "${params.outDir}/VariantCalling/MuTect2", | |||
There was a problem hiding this comment.
So Mutect2 also can be removed.
| @@ -679,7 +659,6 @@ def defineToolList() { | |||
| 'freebayes', | |||
There was a problem hiding this comment.
ditto freebayes though that can be used for germline, so, if somebody wants to have that, s/he can still use it.
There was a problem hiding this comment.
Can we use Freebayes for germline?
We're not doing that yet.
Which settings should we use?
There was a problem hiding this comment.
Aaa, you are right, just remove it.
No description provided.