From 3b4e91d271461093e6b91153260cfaf40a34b86c Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 19 Mar 2021 15:33:03 -0500
Subject: [PATCH] Fix aws batch submit json localtion

---
 .gitlab-ci.yml | 2 +-
 README.md      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7b5a337..819bbfc 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1080,7 +1080,7 @@ aws:
         --job-name nf-GUDMAP_RBK_ci-env\
         --job-queue default-bicf\
         --job-definition nextflow-bicf-nextflow\
-        --container-overrides command=`cat ../docs/nxf_aws-ci-test.json`)
+        --container-overrides command=`cat ./docs/nxf_aws-ci-test.json`)
       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 " " ) &&
diff --git a/README.md b/README.md
index 6bbf831..4ca7db3 100644
--- a/README.md
+++ b/README.md
@@ -104,7 +104,7 @@ This pipeline is also capable of being run on AWS and DNAnexus. To do so:
     --job-name [Job Name]\
     --job-queue [Queue]\
     --job-definition [Job Definition]\
-    --container-overrides command=`cat ../docs/nxf_aws-ci-test.json`
+    --container-overrides command=`cat ./docs/nxf_aws-ci-test.json`
   ```
 ### [DNAnexus](https://dnanexus.com/) (utilizes the [DNAnexus extension package for Nextflow (XPACK-DNANEXUS)](https://github.com/seqeralabs/xpack-dnanexus))
 * Follow the istructions from [XPACK-DNANEXUS](https://github.com/seqeralabs/xpack-dnanexus) about installing and authenticating (a valid license must be available for the extension package from Seqera Labs, as well as a subsription with DNAnexus)
-- 
GitLab