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RGI_MAIN: Replace multiple ifs with a for loop #5614

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May 16, 2024
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RGI_MAIN: Replace multiple ifs with a for loop #5614

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11 changes: 1 addition & 10 deletions modules/nf-core/rgi/main/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -60,16 +60,7 @@ process RGI_MAIN {
--input_sequence $fasta

mkdir temp/
mv *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes temp/

## These files not always generated, so only move if they exist
## Taken from https://stackoverflow.com/a/54655320 (RIP) by @TSJNachos117
if [ "\$(ls -A | grep -i \\variant.json\\\$)" ] ; then mv *variant.json temp/ ; fi
if [ "\$(ls -A | grep -i \\rrna.json\\\$)" ] ; then mv *rrna.json temp/ ; fi
if [ "\$(ls -A | grep -i \\protein.json\\\$)" ] ; then mv *protein.json temp/ ; fi
if [ "\$(ls -A | grep -i \\predictedGenes.json\\\$)" ]; then mv *predictedGenes.json temp/; fi
if [ "\$(ls -A | grep -i \\overexpression.json\\\$)" ]; then mv *overexpression.json temp/; fi
if [ "\$(ls -A | grep -i \\homolog.json\\\$)" ] ; then mv *homolog.json temp/ ; fi
for FILE in *.xml *.fsa *.{nhr,nin,nsq} *.draft *.potentialGenes *{variant,rrna,protein,predictedGenes,overexpression,homolog}.json; do [[ -e \$FILE ]] && mv \$FILE temp/; done

RGI_VERSION=\$(rgi main --version)

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