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Kurt-Hetrick / CIDR_WES

CIDR's production pipeline for WES and other targeted DNA sequencing projects.
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have to add a new condition to find novaseq files that have gone through cram to fastq #66

Closed Kurt-Hetrick closed 5 years ago

Kurt-Hetrick commented 5 years ago

going to have to deal with someday...fastq files will have PU tag nomenclature.

Kurt-Hetrick commented 5 years ago

ugggh...just looked at this to account for now a possible 3rd condition and now i want to vomit...

Kurt-Hetrick commented 5 years ago

for when the bcl2fastq output file nomenclature changes. can do this.

echo du --max-depth=1 -a $FIND_PATH/$SM_TAG* -a $FIND_PATH/$FIXED_PLATFORM_UNIT* 2> /dev/null \| grep "L00"$LANE"_R1_001.fastq" \| cut -f 2 | bash

need to espace the std error redirect like the pipes are being escaped...need to test that

probably want to run this without the stderr redirect to /dev/null for when there is no fastq files....because that is a thing.

still need to work on something for when fastq files are created from bcl2fastq/novaseq cram files.

Kurt-Hetrick commented 5 years ago

theoretically, could use this for all of the things and get rid of the if/else statement (add another -a to look /mnt/research/active/$PROJECT/FASTQ and follow with an egrep to look for both bcl2fastq or $PU.fastq...if a file is found in two places, then I think that it would just take the one that it found last...would have to assume that they are the same-ish (same data but ordered differently)...but I think that would be okay

Kurt-Hetrick commented 5 years ago

done. looks in all the places and takes the last one found.