Commit 97f7ec27 authored by Celine Noirot's avatar Celine Noirot
Browse files

Use and confidg container for mosdepth

parent 5839942b
Pipeline #34202 passed with stages
in 16 minutes and 21 seconds
......@@ -113,4 +113,7 @@ process {
withLabel: eggnog {
container = 'file://metagwgs/env/eggnog_mapper.sif'
}
withLabel: mosdepth {
container = 'file://metagwgs/env/mosdepth.sif'
}
}
......@@ -765,7 +765,7 @@ process depth_on_contigs {
script:
"""
/usr/local/bioinfo/src/mosdepth/mosdepth-v0.2.5/mosdepth -b ${bed} -Q20 -n -x ${replicateId} ${bam}
mosdepth -b ${bed} -Q20 -n -x ${replicateId} ${bam}
"""
}
......
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