diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 0d3f57d4462138b94049bccfb7b8910b3921f9e9..bd1aee4ea8fda6acce19febbec38e0118ed0079b 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -58,7 +58,7 @@ fastqsForce = params.fastqsForce speciesForce = params.speciesForce email = params.email -// Define fixed files +// Define fixed files and replicateExportConfig = Channel.fromPath("${baseDir}/conf/Replicate_For_Input_Bag.json") executionRunExportConfig = Channel.fromPath("${baseDir}/conf/Execution_Run_For_Output_Bag.json") if (params.source == "dev") { @@ -1476,7 +1476,7 @@ process uploadQC { echo LOG: all old mRNA QC RIDs deleted >> ${repRID}.uploadQC.log fi - qc_rid=\$(python3 ${script_deleteEntry_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F) + qc_rid=\$(python3 ${script_uploadQC} -r ${repRID} -e ${executionRunRID} -p "\${end}" -s ${stranded} -l ${length} -w ${rawCount} -f ${finalCount} -o ${source} -c \${cookie} -u F) echo LOG: mRNA QC RID uploaded - \${qc_rid} >> ${repRID}.uploadQC.log echo \${qc_rid} > qcRID.csv