Run sickle on paired end fastq files in parallel. The paired fastq files should be ending on _1.fastq.gz and _2.fastq.gz. The resulting files will be in the current directory with name $base.sickle.{pe1,pe2,se}.fastq. The filenames/directory structure is based on reads delivered by the sequencing facility at SciLifeLab, Sweden to the UPPMAX clus…

parallel_sickle

#!/bin/sh
parallel lib1={}';' \
         lib2='$('echo {} '|' sed s/_1.fastq.gz/_2.fastq.gz/');' \
         base='$('basename {} _1.fastq.gz');' \
         sickle pe -f '$lib1' -r '$lib2' -t sanger \
           -o '$base'.sickle.pe1.fastq \
           -p '$base'.sickle.pe2.fastq \
           -s '$base'.sickle.se.fastq  \
         ::: /proj/b2010008/INBOX/A.Andersson_13_06/*/*/*_1.fastq.gz