Error in GetPileupSummaries when using --no_intervals option

[jfnavarro]

I got this error message

2020-10-23T12:17:09.403+02:00 A USER ERROR has occurred: Argument intervals was missing: Argument 'intervals' is required.

The command executed was:

Command executed:
  gatk --java-options "-Xmx7g"         GetPileupSummaries         -I 3109.recal.bam         -V gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz                  -O no_intervals_3109_pileupsummaries.table
But I can see in the GATK documentation that the argument -L --intervals is required.

But I can see in the GATK documentation that the argument -L --intervals is required.

[priesgo]

GetPileUpSummaries expects in the --intervals parameter the germline resource. This is explained here https://gatk.broadinstitute.org/hc/en-us/articles/360040097432-GetPileupSummaries

So, basically, we will need to pass to --intervals the same parameter that we are passing to --variant.

[priesgo]

Should I take care of doing this one @maxulysse ?

[FriederikeHanssen]

@GCJMackenzie is doing some amazing work on porting the mutect related modules to DSL2 so we can use them in DSL2. Maybe you can take a look there, if it is fixed already :)

[priesgo]

Thanks @FriederikeHanssen will check it there.

[priesgo]

In principle, it seems to be fixed in the module, see here https://github.com/TRON-Bioinformatics/modules/blob/master/modules/gatk4/getpileupsummaries/main.nf#L35

Either the sites or the variants is used, and in no case the --intervals parameter is not provided.

Maybe we could close or maybe we want to add test for this?

[FriederikeHanssen]

Closed by #592