mutect2 fails with --no_intervals option

[lconde-ucl]

Hi,
I'm trying the pipeline (dev version) with some exome data and there seems to be an issue when running it with the "--no_intervals" option. The mutect2 step fails because it tries to use an interval file "-L no_intervals.bed" that does not exist. This is an example .command.sh generated in the mutect2 process:

#!/bin/bash -euo pipefail
# Get raw calls
gatk --java-options "-Xmx7g"  Mutect2  \
-R Homo_sapiens_assembly38.fasta  \
-I NET03-A3_Tumour.recal.bam  -tumor NET03-A3_Tumour   \
-I NET03-A7_Ctr.recal.bam -normal NET03-A7_Ctr      \
-L no_intervals.bed    \
--germline-resource gnomAD.r2.1.1.GRCh38.PASS.AC.AF.only.vcf.gz   \
-O no_intervals_NET03-A3_Tumour_vs_NET03-A7_Ctr.vcf

I understand the reasoning of using the -L argument with the intervals when the pipeline is run in normal mode (i.e., without the --no_intervals" option), but when the user selects the --no-intervals option, shouldn't this be changed so that the -L argument in mutect2 points to the --targetBed file (or nothing for whole genome)?

I guess that what I'm trying to understand too is why the --targetBed targets are being passed to BamQC, manta and strelka, but not to mutect2? Is it because variants called with mutect2 outside the targets are filtered anyway in the concatVCF step later on?

Thanks
Lucia