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Commit 1f7ba7d5 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix stranded test

parent 375d8cad
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2 merge requests!58Develop,!56Resolve "Detect error in inferMetadata for tracking"
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workflow/rna-seq.nf
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...@@ -875,19 +875,21 @@ process checkMetadata { ...@@ -875,19 +875,21 @@ process checkMetadata {
fi fi
if [ "${strandedMeta}" != "${strandedInfer}" ] if [ "${strandedMeta}" != "${strandedInfer}" ]
then then
if [ "${strandedMeta}" == "unstranded" ] pipelineError=true
then pipelineError_stranded=true
pipelineError=true echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
pipelineError_stranded=true if [ "${strandedMeta}" == "stranded" ]
echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
elif [ "${strandedInfer}" != "forward"] || [ "${strandedInfer}" != "reverse" ]
then then
pipelineError=true if [ "${strandedInfer}" == "forward"] || [ "${strandedInfer}" == "reverse" ]
pipelineError_stranded=true then
echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log pipelineError=false
pipelineError_stranded=false
echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
else
echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi
else else
pipelineError_stranded=false echo -e "LOG: stranded does not match: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
echo -e "LOG: stranded matches: Submitted=${strandedMeta}; Infered=${strandedInfer}" >> ${repRID}.checkMetadata.log
fi fi
else else
pipelineError_stranded=false pipelineError_stranded=false
......
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