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Commit cd641050 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix infer with species error

parent d08bd26e
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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...@@ -828,6 +828,7 @@ process inferMetadata { ...@@ -828,6 +828,7 @@ process inferMetadata {
fi fi
if [ "${speciesForce}" != "" ] if [ "${speciesForce}" != "" ]
then then
speciesError=false
echo -e "LOG: species overridden to: ${speciesForce}" echo -e "LOG: species overridden to: ${speciesForce}"
species="${speciesForce}" species="${speciesForce}"
if [ "${speciesForce}" == "Homo sapiens" ] if [ "${speciesForce}" == "Homo sapiens" ]
...@@ -841,7 +842,7 @@ process inferMetadata { ...@@ -841,7 +842,7 @@ process inferMetadata {
fi fi
fi fi
if [ !\${speciesError} ] && [ "${speciesForce}" == "" ] if [ !\${speciesError} ]
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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