Commit c114a629 authored by Gervaise Henry's avatar Gervaise Henry 🤠
Browse files

Reduce species inference cutoffs

parent f0100c48
Pipeline #8303 passed with stages
in 1 minute and 42 seconds
......@@ -599,12 +599,12 @@ process inferMetadata {
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
# determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 25)) ]
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then
species="Homo sapiens"
bam="GRCh.sampled.sorted.bam"
bed="./GRCh/bed/genome.bed"
elif [ 1 -eq \$(echo \$(expr \${align_mo} ">=" 25)) ] && [ 1 -eq \$(echo \$(expr \${align_hu} "<" 25)) ]
elif [ 1 -eq \$(echo \$(expr \${align_mo} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_hu} "<" 40)) ]
then
species="Mus musculus"
bam="GRCm.sampled.sorted.bam"
......
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