Try to fix batch submit command

.gitlab-ci.yml

@@ -1070,9 +1070,10 @@ aws:
     - mkdir -p ./badges/env
     - curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-inactive-critical?style=flat > ./badges/env/aws.svg
     - module load awscli/1.11.139
-    - export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
-    - export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}
-    - aws configure set region ${aws_region}
+    - >
+      export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
+      export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}
+      aws configure set region ${aws_region}
     - aws s3 cp ./test_data/auth/ s3://bicf-output/ci-env/auth/ --exclude "*" --include "c*" --recursive
     - aws s3 cp ./test_data/fastq/xsmall/ s3://bicf-output/ci-env/input/ --exclude "*" --include "Q-Y5F6_10K.R*.fastq.gz" --recursive
     - >
@@ -1080,21 +1081,7 @@ aws:
         --job-name nf-GUDMAP_RBK_ci-env\
         --job-queue default-bicf\
         --job-definition nextflow-bicf-nextflow\
-        --container-overrides command=\
-          "utsw-bicf/gudmap_rbk.rna-seq","-r","env.ci",\
-          "-profile","aws",\
-          "--deriva","s3://bicf-output/ci-env/auth/credential.json",\
-          "--bdbag","s3://bicf-output/ci-env/auth/cookies.txt",\
-          "--repRID","Q-Y5F6",\
-          "--source","staging",\
-          "--upload","false",\
-          "--dev","false",\
-          "--ci","true",\
-          "--track","false",\
-          "-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html",\
-          "--refSource","datahub",\
-          "--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride",\
-          "--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz")
+        --container-overrides command="utsw-bicf/gudmap_rbk.rna-seq","-r","env.ci","-profile","aws","--deriva","s3://bicf-output/ci-env/auth/credential.json","--bdbag","s3://bicf-output/ci-env/auth/cookies.txt","--repRID","Q-Y5F6","--source","staging","--upload","false","--dev","false","--ci","true","--track","false","-with-report","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride_report.html","--refSource","datahub","--outDir","s3://bicf-output/ci-env/output/Q-Y5F6_fastqoverride","--fastqsForce","s3://bicf-output/ci-env/input/*.fastq.gz")
       id=$(echo ${id}| grep -oP "jobId\K.*" | tr -d '"' | tr -d ":" | tr -d " " | tr -d "}")
     - >
       status=$(aws batch describe-jobs --jobs ${id} | grep -oP "status\": \K.*" | tr -d '"' | tr -d ',') &&
@@ -1110,7 +1097,7 @@ aws:
         curl --request GET https://img.shields.io/badge/Envronment%3A%20AWS-run%20failed-critical?style=flat > ./badges/env/dnanexus.svg
       fi
   after_script:
-    - module load awscli/1.19.17
+    - module load awscli/1.11.139
     - >
       export AWS_ACCESS_KEY_ID=${aws_accesskeyid}
       export AWS_SECRET_ACCESS_KEY=${aws_secretaccesskey}