Add back consistent test

.gitlab-ci.yml

@@ -1011,6 +1011,24 @@ override_spike:
       - always
 
 
+consistency:
+  stage: consistency
+  only: [merge_requests]
+  except:
+    variables:
+        - $CI_MERGE_REQUEST_TARGET_BRANCH_NAME =~ /master/
+  script:
+    - pytest -m consistencySE
+    - pytest -m consistencyPE
+  artifacts:
+    name: "$CI_JOB_NAME"
+    when: always
+    paths:
+      - SE_multiqc_data.json
+      - PE_multiqc_data.json
+    expire_in: 7 days
+
+
 dnanexus:
   stage: environment
   only:
@@ -1080,7 +1098,7 @@ 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=$(envsubst < ./docs/nxf_aws-ci-test.json))
       id=$(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 " " ) &&

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=$(envsubst < ./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)

nextflowConf/aws.config

@@ -4,10 +4,12 @@ params {
 
 process {
   withName:trackStart {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:getBag {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
@@ -16,6 +18,7 @@ process {
     memory = '32 GB'
   }
   withName:parseMetadata {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
@@ -32,6 +35,7 @@ process {
     memory = '32 GB'
   }
   withName:seqwho {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
@@ -40,6 +44,7 @@ process {
     memory = '32 GB'
   }
   withName:downsampleData {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
@@ -56,6 +61,7 @@ process {
     memory = '32 GB'
   }
   withName:checkMetadata {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
@@ -80,42 +86,52 @@ process {
     memory = '32 GB'
   }
   withName:aggrQC {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadInputBag {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadExecutionRun {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadQC {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadProcessedFile {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadOutputBag {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:finalizeExecutionRun {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:failPreExecutionRun {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:failExecutionRun {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }
   withName:uploadQC_fail {
+    executor = 'local'
     cpus = 1
     memory = '1 GB'
   }