Possible unneeded output files

[johnegarza]

docker-immuno_tools-cwl/optitype_script.sh

Lines 48 to 49 in ef53b1e

	cat $TEMPDIR/$name.aln.map.fwd.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > $outdir/$name.hla.fwd.fastq
	cat $TEMPDIR/$name.aln.map.rev.sam | grep -v ^@ | awk '{print "@"$1"\n"$10"\n+\n"$11}' > $outdir/$name.hla.rev.fastq

These lines were left unchanged from the original version of the script. They generate fastq files that are placed in the output directory, unlike the temporary directory like all other non-optitype output files. Also unlike those files, they are also never cleaned up with an rm line. Is this intended, and should they be kept there and included in the cwl output, or can they be cleaned up?