CODEWITHSUNDEEP
bash
justaguy
justaguy

Reputation: 3022

bash loop writing over next file

I am trying to process multiple bam files in a loop using the standard and having an issue where each file overwrites the other. The --bam xxx \ is the only line that will change and the xxx depends on the bam files in the directory. In this example there are three, but that is not always the case. Thank you :).

files in directory --- won't always be three ---

xxx_00.bam
yyy_01.bam
zzz_02.bam

standard

for bam in *.bam ; do
 ${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py \
   --bam ${bam} \
   --referenceFasta $fasta \
   --callRegions $bed \
   --exome
   --runDir $dir
 $dir/runWorkflow.py -m local -j 20
done

desired

for bam in *.bam ; do
 ${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py \
   --bam ${bam} \   --- xxx_00.bam ---
   --bam ${bam} \   --- yyy_01.bam ---
   --bam ${bam} \   --- zzz_02.bam ---
   --referenceFasta $fasta \
   --calRegions $bed \
   --exome \
   --runDir $dir
 $dir/runWorkflow.py -m local -j 20
done

Tried --- prints the desired but does not execute it ---

printf -- "${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py \\\\\n%s\n\t\t--referenceFasta $fasta \\\\\n\t\t--callRegions $bed \\\\\n\t\t--exome \\\\\n\t\t--runDir ${dir}\n" \
"$(for f in *.bam; do printf -- "\t\t--bam %s \\\\\n"    "${f}"; done)"
${dir}/runWorkflow.py -m local -j 20

Upvotes: 0

Views: 78

Answers (1)

Paul Hodges
Paul Hodges

Reputation: 15293

Doesn't look to me like you need the loop at all.

${path_to_strelka}/bin/configureStrelkaGermlineWorkflow.py \
    $( printf " --bam %s " *bam ) \
   --referenceFasta $fasta \
   --calRegions $bed \
   --exome \
   --runDir $dir \
$dir/runWorkflow.py -m local -j 20

Upvotes: 2

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