From 9b65a0eac1f3e919d783b6aa68b4eb1372807960 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 12 Apr 2021 20:54:54 -0500
Subject: [PATCH] Replace track
---
rna-seq.nf | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
diff --git a/rna-seq.nf b/rna-seq.nf
index c04fa39..9f4be25 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -113,6 +113,47 @@ script_deleteEntry_uploadQC = Channel.fromPath("${baseDir}/workflow/scripts/dele
script_deleteEntry_uploadQC_fail = Channel.fromPath("${baseDir}/workflow/scripts/delete_entry.py")
script_deleteEntry_uploadProcessedFile = Channel.fromPath("${baseDir}/workflow/scripts/delete_entry.py")
+/*
+ * trackStart: track start of pipeline
+ */
+process trackStart {
+ script:
+ """
+ hostname
+ ulimit -a
+
+ curl -H 'Content-Type: application/json' -X PUT -d \
+ '{ \
+ "sessionId": "${workflow.sessionId}", \
+ "pipeline": "gudmap.rbk_rnaseq", \
+ "start": "${workflow.start}", \
+ "repRID": "${repRID}", \
+ "astrocyte": false, \
+ "status": "started", \
+ "nextflowVersion": "${workflow.nextflow.version}", \
+ "pipelineVersion": "${workflow.manifest.version}", \
+ "ci": ${params.ci}, \
+ "dev": ${params.dev} \
+ }' \
+ "https://xku43pcwnf.execute-api.us-east-1.amazonaws.com/ProdDeploy/pipeline-tracking"
+
+ if [ ${params.track} == true ]
+ then
+ curl -H 'Content-Type: application/json' -X PUT -d \
+ '{ \
+ "ID": "${workflow.sessionId}", \
+ "repRID": "${repRID}", \
+ "PipelineVersion": "${workflow.manifest.version}", \
+ "Server": "${params.source}", \
+ "Queued": "NA", \
+ "CheckedOut": "NA", \
+ "Started": "${workflow.start}" \
+ }' \
+ "https://9ouc12dkwb.execute-api.us-east-2.amazonaws.com/prod/db/track"
+ fi
+ """
+}
+
log.info """\
====================================
BICF RNA-seq Pipeline for GUDMAP/RBK
--
GitLab