From 4037ad2c674bcb631b70f86833c258c4fa580d62 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 12 Apr 2021 20:44:21 -0500
Subject: [PATCH] Temporarily change aws env test to use dev
---
rna-seq.nf | 41 -----------------------------------------
1 file changed, 41 deletions(-)
diff --git a/rna-seq.nf b/rna-seq.nf
index 9f4be25..c04fa39 100644
--- a/rna-seq.nf
+++ b/rna-seq.nf
@@ -113,47 +113,6 @@ 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