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Irma sif #8

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merged 2 commits into from
Jun 20, 2024
+6 −5
Merged

Irma sif #8

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bc58150
pulling IRMA out of container to avoid issues
DOH-JDJ0303 Jun 20, 2024
ed295e3
copy IRMA from container (fix #7)
Jun 20, 2024
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11 changes: 6 additions & 5 deletions modules/local/irma.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@ process IRMA {
stageInMode 'copy'

container "docker.io/staphb/irma:1.1.4"
containerOptions = "${ workflow.containerEngine == 'singularity' || workflow.containerEngine == 'apptainer' ? '--writable-tmpfs' : '' }"

input:
tuple val(meta), path(refs), path(reads)
Expand All @@ -25,8 +24,10 @@ process IRMA {
prefix = "${meta.id}"

"""
# determine IRMA path
# copy IRMA to workdir
irma_path=\$(which IRMA)
cp -r \${irma_path%IRMA} ./
irma_path="\$(dirname \${irma_path#/})/IRMA"

# create module
mod=\$(shuf -er -n20 {A..Z} {a..z} {0..9} | tr -d '\n')
Expand Down Expand Up @@ -56,7 +57,7 @@ process IRMA {
esac
## set QC thresholds
echo -e 'MIN_AMBIG=${params.cons_ratio}\nMIN_CONS_SUPPORT=${params.cons_depth}\nMIN_CONS_QUALITY=${params.cons_qual}\nDEL_TYPE=${ params.cons_amb == 'N' ? 'NNN' : params.cons_amb }' >> irma.config
# set elongation option
## set elongation option
echo -e 'SKIP_E=${ params.cons_elong ? '1' : '0' }' >> irma.config

# combine references into single file
Expand All @@ -71,7 +72,7 @@ process IRMA {
done

# run IRMA
IRMA \${mod} --external-config irma.config ${reads[0]} ${reads[1]} results
\$irma_path \${mod} --external-config irma.config ${reads[0]} ${reads[1]} results

# rename assemblies
for F in \$(ls results/*.fasta)
Expand All @@ -87,6 +88,6 @@ process IRMA {
done

# clean up
rm -r \${irma_path}_RES/modules/\${mod}
#rm -r \${irma_path}_RES/modules/\${mod}
"""
}
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