diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index 32e3c26c714a5969ee903b336f680e4758c4997e..69c3a2d39fd4dff4d1be9362c65683f44799c833 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -138,7 +138,7 @@ process trackStart { }' \ "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking" - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then curl -H 'Content-Type: application/json' -X PUT -d \ '{ \ @@ -1442,7 +1442,7 @@ process uploadExecutionRun { echo "\${executionRun_rid}" > executionRunRID.csv - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then curl -H 'Content-Type: application/json' -X PUT -d \ '{ \ @@ -2056,7 +2056,7 @@ process aggrQC { multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then curl -H 'Content-Type: application/json' -X PUT -d \ @./${repRID}.multiqc_data.json \ @@ -2345,7 +2345,7 @@ process finalizeExecutionRun { rid=\$(python3 ${script_uploadExecutionRun_finalizeExecutionRun} -r ${repRID} -w \${workflow} -g \${genome} -i ${inputBagRID} -s Success -d 'Run Successful' -o ${source} -c \${cookie} -u ${executionRunRID}) echo LOG: execution run RID marked as successful - \${rid} >> ${repRID}.finalizeExecutionRun.log - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then dt=`date +%FT%T.%3N%:z` curl -H 'Content-Type: application/json' -X PUT -d \ @@ -2450,7 +2450,7 @@ process failPreExecutionRun { echo "\${rid}" > executionRunRID.csv - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then dt=`date +%FT%T.%3N%:z` curl -H 'Content-Type: application/json' -X PUT -d \ @@ -2552,7 +2552,7 @@ process failExecutionRun { echo LOG: execution run RID marked as error - \${rid} >> ${repRID}.failExecutionRun.log fi - if [ ${prarams.track} == true ] + if [ ${params.track} == true ] then dt=`date +%FT%T.%3N%:z` curl -H 'Content-Type: application/json' -X PUT -d \