Typo for Mutect2

[FriederikeHanssen]

When running sarek 2.6.1 with:

nextflow run nf-core/sarek -profile cfc -r 2.6.1 \
--outdir 'sarek_patients_1_10' \
--input 'sarek_patients_1_10.tsv' \
--genome 'GRCh38' \
--tools 'Strelka,ASCAT,snpEff,Mutect2' \
-c sarek.config \
--no_gatk_spark \
-resume

I get:

 No such variable: variantcaller
 -- Check script '/home-link/iizha01/.nextflow/assets/nf-core/sarek/main.nf' at line: 3387 or see '.nextflow.log' file for more details

The respective line is:

variantCaller, idPatient, idSample, vcf, tbi, tsv ->

Embedded within:

vcfKeep = Channel.empty().mix(
    filteredMutect2Output.map{
        variantCaller, idPatient, idSample, vcf, tbi, tsv ->
        [variantcaller, idSample, vcf]
    },
    vcfConcatenated.map{
        variantcaller, idPatient, idSample, vcf, tbi ->
        [variantcaller, idSample, vcf]
    },

I think it is a typo in the variable variantCaller and should be variantcaller instead.

[maxulysse]

Good spot, sorry about that.
We can find a solution (ie quick release during the hackathon if needed).

[FriederikeHanssen]

@maxulysse no problem :) I am running the pipeline without Mutect now. But sure, would be great to include in future runs :)