How to add prefix to samtools collate

Question

[MAPK]

I am trying to run this command in loop. While doing so I am getting error for tmp directory having no space in collate step. I saw that samtools manual mentioning about prefix, but I am not sure how to redirect to temporary files to desired /path using prefix.

samtools collate -uO ${INBAM} | samtools fastq - -@ ${THREADS} -N -1 ${FQ_OUT1} -2 ${FQ_OUT2} -0 /dev/null -s /dev/null -n

What do I need to do to direct any temporary data to my designated /path?

Answer 1

[ATpoint]

Usage: samtools collate [-Ou] [-o <name>] [-n nFiles] [-l cLevel] <in.bam> [<prefix>]

samtools collate -uO ${INBAM} ${INBAM}_prefix | samtools fastq - -@ ${THREADS} -N -1 ${FQ_OUT1} -2 ${FQ_OUT2} -0 /dev/null -s /dev/null -n