From ff3c51461c1f4a28e0a288036458fc2446aefbaf Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 12 Apr 2021 12:55:19 -0500
Subject: [PATCH] Shorten aws status check
---
.gitlab-ci.yml | 6 ++++--
nextflow.config | 16 ----------------
2 files changed, 4 insertions(+), 18 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5667086..364ea11 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1102,10 +1102,12 @@ aws:
id=$(echo ${id}| grep -oP "jobId\K.*" | tr -d '"' | tr -d ":" | tr -d " " | tr -d "}")
- >
status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',' | tr -d " " ) &&
- until [[ "${status}" == "SUCCEEDED" || "${status}" == "FAILED" ]]; do
+ until [[ "${status}" == "SUCCEEDED" ] || [ "${status}" == "FAILED" ]]; do
status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',' | tr -d " " ) &&
echo ${status} &&
- sleep 5m
+ if [[ "${status}" != "SUCCEEDED" && "${status}" != "FAILED" ]]; then
+ sleep 1m
+ fi
done
- >
if [ "${status}" == "SUCCEEDED" ]; then
diff --git a/nextflow.config b/nextflow.config
index 53ead0e..5406cc2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -106,22 +106,6 @@ process {
}
}
-trace {
- enabled = false
- file = 'trace.txt'
- fields = 'task_id,native_id,process,name,status,exit,submit,start,complete,duration,realtime,%cpu,%mem,rss'
-}
-
-timeline {
- enabled = false
- file = 'timeline.html'
-}
-
-report {
- enabled = false
- file = 'report.html'
-}
-
tower {
accessToken = '3ade8f325d4855434b49aa387421a44c63e3360f'
enabled = true
--
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