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Commit f59cda49 authored by Gervaise Henry's avatar Gervaise Henry 🤠
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Fix fail on ambiguous species

parent 6d6ff73a
2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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workflow/rna-seq.nf
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...@@ -840,36 +840,44 @@ process inferMetadata { ...@@ -840,36 +840,44 @@ process inferMetadata {
fi fi
fi fi
# infer experimental setting from dedup bam if [ !\${speciesError} ] && [ "${speciesForce}" = "" ]
echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt
echo -e "LOG: inferred" >> ${repRID}.inferMetadata.log
ended=`bash ${script_inferMeta} endness ${repRID}.infer_experiment.txt`
fail=`bash ${script_inferMeta} fail ${repRID}.infer_experiment.txt`
if [ \${ended} == "PairEnd" ]
then then
ends="pe" # infer experimental setting from dedup bam
percentF=`bash ${script_inferMeta} pef ${repRID}.infer_experiment.txt` echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
percentR=`bash ${script_inferMeta} per ${repRID}.infer_experiment.txt` infer_experiment.py -r "\${bed}" -i "\${bam}" 1>> ${repRID}.infer_experiment.txt
elif [ \${ended} == "SingleEnd" ] echo -e "LOG: inferred" >> ${repRID}.inferMetadata.log
then
ends="se" ended=`bash ${script_inferMeta} endness ${repRID}.infer_experiment.txt`
percentF=`bash ${script_inferMeta} sef ${repRID}.infer_experiment.txt` fail=`bash ${script_inferMeta} fail ${repRID}.infer_experiment.txt`
percentR=`bash ${script_inferMeta} ser ${repRID}.infer_experiment.txt` if [ \${ended} == "PairEnd" ]
fi then
echo -e "LOG: percentage reads in the same direction as gene: \${percentF}" >> ${repRID}.inferMetadata.log ends="pe"
echo -e "LOG: percentage reads in the opposite direction as gene: \${percentR}" >> ${repRID}.inferMetadata.log percentF=`bash ${script_inferMeta} pef ${repRID}.infer_experiment.txt`
if [ 1 -eq \$(echo \$(expr \${percentF#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentR#*.} "<" 2500)) ] percentR=`bash ${script_inferMeta} per ${repRID}.infer_experiment.txt`
then elif [ \${ended} == "SingleEnd" ]
stranded="forward" then
elif [ 1 -eq \$(echo \$(expr \${percentR#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentF#*.} "<" 2500)) ] ends="se"
then percentF=`bash ${script_inferMeta} sef ${repRID}.infer_experiment.txt`
stranded="reverse" percentR=`bash ${script_inferMeta} ser ${repRID}.infer_experiment.txt`
fi
echo -e "LOG: percentage reads in the same direction as gene: \${percentF}" >> ${repRID}.inferMetadata.log
echo -e "LOG: percentage reads in the opposite direction as gene: \${percentR}" >> ${repRID}.inferMetadata.log
if [ 1 -eq \$(echo \$(expr \${percentF#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentR#*.} "<" 2500)) ]
then
stranded="forward"
elif [ 1 -eq \$(echo \$(expr \${percentR#*.} ">" 2500)) ] && [ 1 -eq \$(echo \$(expr \${percentF#*.} "<" 2500)) ]
then
stranded="reverse"
else
stranded="unstranded"
fi
echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
else else
stranded="unstranded" ends=""
stranded=""
spike=""
species=""
fi fi
echo -e "LOG: stradedness set to: \${stranded}" >> ${repRID}.inferMetadata.log
# write inferred metadata to file # write inferred metadata to file
echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv echo "\${ends},\${stranded},\${spike},\${species},\${align_ercc},\${align_hu},\${align_mo},\${percentF},\${percentR},\${fail}" 1>> infer.csv
......
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