diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf index dc09f8d525b3b592a25ba3af48c6204da33e7a6c..eff87e6cd79a35895fff93ac386a1b5b3d9af9f0 100644 --- a/workflow/rna-seq.nf +++ b/workflow/rna-seq.nf @@ -1255,6 +1255,13 @@ process uploadExecutionRun { fi echo "\${executionRun_rid}" > executionRunRID.csv + + curl -H 'Content-Type: application/json' -X PUT -d \ + '{ \ + "ID": "${workflow.sessionId}" \ + "ExecutionRunRID": "\${executionRun_rid}" \ + }' \ + "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track" """ } @@ -1868,7 +1875,12 @@ process aggrQC { echo -e "LOG: running multiqc" >> ${repRID}.aggrQC.log multiqc -c ${multiqcConfig} . -n ${repRID}.multiqc.html cp ${repRID}.multiqc_data/multiqc_data.json ${repRID}.multiqc_data.json - """ + + rpt=`cat ${repRID}.multiqc_data.json` + curl -H 'Content-Type: application/json' -X PUT -d \ + \${rpt} \ + "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/qc" + """ } /* @@ -1935,11 +1947,6 @@ process uploadQC { echo LOG: mRNA QC RID uploaded - \${qc_rid} >> ${repRID}.uploadQC.log echo "\${qc_rid}" > qcRID.csv - - rpt=`cat ${repRID}.multiqc_data.json` - curl -H 'Content-Type: application/json' -X PUT -d \ - \${rpt} - "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/qc" """ } @@ -2152,12 +2159,11 @@ process finalizeExecutionRun { dt=`date --utc +%FT%TZ` curl -H 'Content-Type: application/json' -X PUT -d \ '{ \ - "ID": "${workflow.sessionId}" + "ID": "${workflow.sessionId}" \ "Complete": "\${dt}" \ }' \ "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track" """ - """ } /* @@ -2243,7 +2249,7 @@ process failPreExecutionRun { dt=`date --utc +%FT%TZ` curl -H 'Content-Type: application/json' -X PUT -d \ '{ \ - "ID": "${workflow.sessionId}" + "ID": "${workflow.sessionId}" \ "Failure": "\${dt}" \ }' \ "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track" @@ -2334,7 +2340,7 @@ process failExecutionRun { dt=`date --utc +%FT%TZ` curl -H 'Content-Type: application/json' -X PUT -d \ '{ \ - "ID": "${workflow.sessionId}" + "ID": "${workflow.sessionId}" \ "Failure": "\${dt}" \ }' \ "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"