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Commit 7c606bac authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix infer metadata

parent 2c26323b
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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...@@ -804,6 +804,7 @@ process inferMetadata { ...@@ -804,6 +804,7 @@ process inferMetadata {
echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log
speciesError=false speciesError=false
speciesError_details=""
# determine species # determine species
if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ] if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ]
then then
...@@ -840,7 +841,7 @@ process inferMetadata { ...@@ -840,7 +841,7 @@ process inferMetadata {
fi fi
fi fi
if [ "\${speciesError" == false ] && [ "${speciesForce}" = "" ] if [ \${speciesError} ] && [ "${speciesForce}" = "" ]
then then
# infer experimental setting from dedup bam # infer experimental setting from dedup bam
echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log
......
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