ds-cgpwgs.pl -sp not carried over to cgpFlagCaVEMan.pl -s

[ym3]

dockstore-cgpwgs-2.1.0 falls over on mouse bam files mapped using dockstore-cgpmap-3.0.4 giving these errors:

No flagList found in flag.vcf.config.WGS.ini for section MUS MUSCULUS_WGS FLAGLIST. No flagging will be done. at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl line 822.

No config found in flag.vcf.config.WGS.ini for section MUS MUSCULUS_WGS FLAGLIST at /opt/wtsi-cgp/bin/cgpFlagCaVEMan.pl line 829.

I am using mm10 reference bundle both for mapping and variant calling.

I am running like ds-cgpwgs.pl -sp mouse -as mm10 but as the bam files have "SP:Mus musculus" in their @SQ header lines, this is carried over to cgpFlagCaVEMan.pl -s 'Mus musculus' which fails as the reference file flag.vcf.config.WGS.ini does not have the flagList or prams for 'Mus musculus'.

The behaviour should be that -sp from ds-cgpwgs.pl should override SP: in the bam headers so the flagging would run like this: cgpFlagCaVEMan.pl -s mouse