Revert to layered configs

.gitlab-ci.yml

@@ -40,7 +40,7 @@ simple_1:
       - develop
       - master
   script:
-  - 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'
+  - 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'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -65,7 +65,7 @@ simple_2:
       - master
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/mu.v3s1r500/*.fastq.gz" --designFile "test_data/mu.v3s1r500/design.csv" --genome 'mm10-3.0.0' --kitVersion '3GEXv3' --version '3.1.0'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -89,7 +89,7 @@ detailed_1:
     refs:
       - tags
   script:
-  - 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'
+  - 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'
   - pytest -m count310
   artifacts:
     name: "$CI_JOB_NAME"
@@ -114,7 +114,7 @@ detailed_2:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v3s2r10k/*.fastq.gz" --designFile "test_data/hu.v3s2r10k/design.csv" --genome 'GRCh38-3.0.0' --kitVersion 'auto' --version '3.0.2'
   - pytest -m count302
   artifacts:
     name: "$CI_JOB_NAME"
@@ -138,7 +138,7 @@ detailed_3:
     refs:
       - tags
   script:
-  - 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'
+  - 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'
   - pytest -m count301
   artifacts:
     name: "$CI_JOB_NAME"
@@ -162,7 +162,7 @@ detailed_4:
     refs:
       - tags
   script:
-  - nextflow -q run workflow/main.nf -profile biohpc_cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
+  - nextflow -q run workflow/main.nf -profile biohpc,cluster --fastq "test_data/hu.v2s2r10k/*.fastq.gz" --designFile "test_data/hu.v2s2r10k/design.csv" --genome 'GRCh38-1.2.0' --kitVersion 'two' --version '2.1.1'
   - pytest -m count211
   artifacts:
     name: "$CI_JOB_NAME"

workflow/conf/biohpc_local.config → workflow/conf/biohpc.config

-process {
-  executor = 'local'
-
-  withLabel: checkDesignFile {
-    module = ['python/3.6.1-2-anaconda']
-  }
-  withLabel: count211 {
-    module = ['cellranger/2.1.1']
-  }
-  withLabel: count301 {
-    module = ['cellranger/3.0.1']
-  }
-  withLabel: count302 {
-    module = ['cellranger/3.0.2']
-  }
-  withLabel: count310 {
-    module = ['cellranger/3.1.0']
-  }
-  withLabel: versions {
-    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-  }
-  withLabel: multiqc {
-    module = ['multiqc/1.7']
-  }
-}
-
 params {
   // Reference file paths on BioHPC
   genomes {

workflow/conf/biohpc_cluster.config → workflow/conf/cluster.config

@@ -5,7 +5,6 @@ process {
 
   withLabel: checkDesignFile {
     module = ['python/3.6.1-2-anaconda']
-    queue = '32GB'
   }
   withLabel: count211 {
     module = ['cellranger/2.1.1']
@@ -25,64 +24,8 @@ process {
   }
   withLabel: versions {
     module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
-    queue = '32GB'
   }
   withLabel: multiqc {
     module = ['multiqc/1.7']
-    queue = '32GB'
-  }
-}
-
-params {
-  // Reference file paths on BioHPC
-  genomes {
-    'GRCh38-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'GRCh38_and_mm10-3.1.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-3.0.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'hg19_and_mm10-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-    'ercc92-1.2.0' {
-      loc = '/project/apps_database/cellranger/refdata-cellranger-'
-    }
-  }
-  // Chemistry mapping parameter
-  chemistry {
-    'auto' {
-      param = 'auto'
-    }
-    '3GEXv1' {
-      param = 'SC3Pv1'
-    }
-   '3GEXv2' {
-      param = 'SC3Pv2'
-    }
-   '3GEXv3' {
-      param = 'SC3Pv3'
-    }
-   '5GEX' {
-      param = 'fiveprime'
-    }
   }
 }

workflow/conf/local.config

+process {
+  executor = 'local'
+
+  withLabel: checkDesignFile {
+    module = ['python/3.6.1-2-anaconda']
+  }
+  withLabel: count211 {
+    module = ['cellranger/2.1.1']
+  }
+  withLabel: count301 {
+    module = ['cellranger/3.0.1']
+  }
+  withLabel: count302 {
+    module = ['cellranger/3.0.2']
+  }
+  withLabel: count310 {
+    module = ['cellranger/3.1.0']
+  }
+  withLabel: versions {
+    module = ['python/3.6.1-2-anaconda','pandoc/2.7','multiqc/1.7']
+  }
+  withLabel: multiqc {
+    module = ['multiqc/1.7']
+  }
+}

workflow/nextflow.config

 profiles {
-  biohpc_local {
-    includeConfig 'conf/biohpc_local.config'
+  biohpc {
+    includeConfig 'conf/biohpc.config'
   }
-  biohpc_cluster {
-    includeConfig 'conf/biohpc_cluster.config'
+  local {
+    includeConfig 'conf/local.config'
+  }
+  cluster {
+    includeConfig 'conf/cluster.config'
   }
   aws {
     includeConfig 'conf/aws.config'