Remove explicit config and try replacing -bg with -q

.gitlab-ci.yml

@@ -40,7 +40,7 @@ simple_1:
       - develop
       - master
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s1r500/*.fastq.gz" --designFile "test_data/hu.v3s1r500/design.csv" --genome 'GRCh38-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -64,7 +64,7 @@ simple_2:
       - master
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -87,7 +87,7 @@ detailed_1:
     refs:
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc,_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc,_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.1.0'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -111,7 +111,7 @@ detailed_2:
     refs:
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -134,7 +134,7 @@ detailed_3:
     refs:
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
+  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s2r10k/*.fastq.gz" --designFile "test_data/mu.v3s2r10k/design.csv" --genome 'mm10-3.0.0' --kitVersion 'three' --version '3.0.1'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always
@@ -157,7 +157,7 @@ detailed_4:
     refs:
       - tags
   script:
-  - nextflow -bg run workflow/main.nf -config workflow/nextflow.config -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
   artifacts:
     name: "$CI_JOB_NAME"
     when: always

workflow/conf/biohpc_cluster.config

@@ -5,7 +5,7 @@ process {
 
   withLabel: checkDesignFile {
     module = ['python/3.6.1-2-anaconda']
-    executor = 'local'
+    queue = '32GB'
   }
   withLabel: count211 {
     module = ['cellranger/2.1.1']
@@ -25,11 +25,11 @@ process {
   }
   withLabel: versions {
     module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-    executor = 'local'
+    queue = '32GB'
   }
   withLabel: multiqc {
     module = ['multiqc/1.7']
-    executor = 'local'
+    queue = '32GB'
   }
 }