bash - Linux for loop for 2 inputs and 4 outputs -

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i need write for loop.

input: file01_r1.fastq, file01_r2.fastq. have 100 files e.g., file02_r1.fastq, file02_r2.fastq , on.

output: file01_r1_pe.fastq, file01_r1_se.fastq, file01_r2_pe.fastq, file01_r2_se.fastq

i need write loop can run executable 100 files. please!

i assume given file 

file01_r1.fastq

you want run:

trimmomatic file01_r1.fastq file01_r2.fastq -o file01_r1_pe.fastq file01_r1_se.fastq file01_r2_pe.fastq file01_r2_se.fastq

using gnu parallel looks this:

parallel trimmomatic {} {= s/_r1/_r2/ =} -o {= s/_r1/_r1_pe/ =} {= s/_r1/_r1_se/ =} {= s/_r1/_r2_pe/ =} {= s/_r1/_r2_se/ =} ::: *_r1.fastq

gnu parallel general parallelizer , makes easy run jobs in parallel on same machine or on multiple machines have ssh access to.

if have 32 different jobs want run on 4 cpus, straight forward way parallelize run 8 jobs on each cpu:

simple scheduling

gnu parallel instead spawns new process when 1 finishes - keeping cpus active , saving time:

gnu parallel scheduling

installation

if gnu parallel not packaged distribution, can personal installation, not require root access. can done in 10 seconds doing this:

(wget -o - pi.dk/3 || curl pi.dk/3/ || fetch -o - http://pi.dk/3) | bash

for other installation options see http://git.savannah.gnu.org/cgit/parallel.git/tree/readme

learn more

see more examples: http://www.gnu.org/software/parallel/man.html

watch intro videos: https://www.youtube.com/playlist?list=pl284c9ff2488bc6d1

walk through tutorial: http://www.gnu.org/software/parallel/parallel_tutorial.html

sign email list support: https://lists.gnu.org/mailman/listinfo/parallel


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