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

Replies to Re: Re: nested for loop rss

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Re: Re: Re: nested for loop Eratic Horse bash 2 Years ago.
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