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

[keiranmraine]

Have you tried:

ds-cgpwgs.pl -sp 'Mus musculus' -as mm10...

I think this works, however I can't say for certain. The wrapper code rewrites the flag.vcf.config.WGS.ini based on what you provide on the wrapper script command line.

dockstore-cgpwgs/scripts/ds-cgpwgs.pl

Lines 179 to 193 in 22a637f

	sub add_species_flag_ini {
	my ($species, $ini_in) = @_;
	$species =~ s/ /_/g;
	$species = uc $species;
	my $ini_out = $opts{'o'}.'/flag.vcf.config.WGS.ini';
	open my $IN, '<', $ini_in;
	open my $OUT,'>',$ini_out;
	while(my $line = <$IN>) {
	$line =~ s/^\[HUMAN_/[${species}_/;
	print $OUT $line;
	}
	close $OUT;
	close $IN;
	return $ini_out;
	}

The error showing MUS MUSCULUS_WGS FLAGLIST rather than MUS_MUSCULUS_WGS FLAGLIST suggests this may still fail (as the above code shows the space being substituted).

Theoretically updating this function to always defer to the provided value (when specified) should solve this:

dockstore-cgpwgs/scripts/ds-cgpwgs.pl

Lines 147 to 177 in 22a637f

	sub resolve_sp_as {
	my $options = shift;
	## read species/assembly from bam headers
	my ($mt_species, $mt_assembly) = species_assembly_from_xam($options->{'t'});
	my ($wt_species, $wt_assembly) = species_assembly_from_xam($options->{'n'});
	if($mt_species ne $wt_species) {
	warn "WARN: Species mismatch between T/N [CR|B]AM headers\n";
	if(!defined $options->{'sp'} || $options->{'sp'} eq q{}) {
	die "ERROR: Please define species to handle this mismatch\n";
	}
	}
	elsif($mt_species ne q{}) {
	$options->{'sp'} = $mt_species;
	}
	if(!defined $options->{'sp'} || $options->{'sp'} eq q{}) {
	die "ERROR: Please define species, not found in [CR|B]AM headers.\n";
	}
	if($mt_assembly ne $wt_assembly) {
	warn "WARN: Assembly mismatch between T/N [CR|B]AM headers\n";
	if(!defined $options->{'as'} || $options->{'as'} eq q{}) {
	die "ERROR: Please define assembly to handle this mismatch\n";
	}
	}
	elsif($mt_assembly ne q{}) {
	$options->{'as'} = $mt_assembly;
	}
	if(!defined $options->{'as'} || $options->{'as'} eq q{}) {
	die "ERROR: Please define assembly, not found in [CR|B]AM headers.\n";
	}
	}

Unfortunately I don't know when we would be able to perform a full round of testing, feel free to raise a PR.

[ym3]

Thanks for your input.
This was easily solved by simply adding the corresponding parameters and flags
[MUS MUSCULUS_WGS PARAMS]
[MUS MUSCULUS_WGS FLAGLIST]
[MUS MUSCULUS_WGS BEDFILES]
to flag.vcf.config.WGS.ini file which makes part of SNV_INDEL_mm10-fragment.tar.gz that is supplied to ds-cgpwgs.pl using -si option.