Compress profile configs

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

workflow/conf/biohpc_cluster.config

@@ -32,3 +32,57 @@ process {
     executor = 'local'
   }
 }
+
+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/biohpc_local.config

@@ -22,4 +22,58 @@ process {
   withLabel: multiqc {
     module = ['multiqc/1.7']
   }
-}
\ No newline at end of file
+}
+
+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/nextflow.config

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