From Small Owl, 3 Years ago, written in Bash.
This paste is a reply to Re: Re: Re: Re: Re: nested for loop from Paltry Tern - view diff
  1. #!/bin/bash
  2.  
  3. while read -r line; do
  4.   bwa samse /ref/refgenome.fa
  5.     "$HOME/gbs/fastq/Round2/stacks/aln/lane2/$line.fq.gz.sai"
  6.     "$HOME/gbs/fastq/Round2/stacks/samples/Lane2/$line.fq.gz"
  7.     | tee "$HOME/gbs/fastq/Round2/stacks/aln/sam/lane2/$line.sam"
  8.           "$HOME/gbs/fastq/Round2/stacks/aln/sam/lane2/${line}_sam.log"
  9. done < ~/gbs/fastq/Round2/stacks/aln/lane2/lane2.files

Replies to Re: Re: Re: Re: Re: Re: nested for loop rss

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Re: Re: Re: Re: Re: Re: Re: nested for loop Soft Tern bash 3 Years ago.
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