diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index e3cbcbe23427f85708fe478d4a4cb82d4fc7bfdd..a17b8bc4f3bdf6907ae1884c87186dd8605ce6af 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -804,6 +804,7 @@ process inferMetadata { echo -e "LOG: inference of strandedness results is: \${spike}" >> ${repRID}.inferMetadata.log speciesError=false + speciesError_details="" # determine species if [ 1 -eq \$(echo \$(expr \${align_hu} ">=" 40)) ] && [ 1 -eq \$(echo \$(expr \${align_mo} "<" 40)) ] then @@ -840,7 +841,7 @@ process inferMetadata { fi fi - if [ "\${speciesError" == false ] && [ "${speciesForce}" = "" ] + if [ \${speciesError} ] && [ "${speciesForce}" = "" ] then # infer experimental setting from dedup bam echo -e "LOG: infer experimental setting from dedup bam" >> ${repRID}.inferMetadata.log