Merge branch '2-ref.genome.folder' into 'develop'

Resolve "Remove reference genome full folder"

Closes #2

See merge request !9

astrocyte_pkg.yml

@@ -97,15 +97,15 @@ workflow_parameters:
   - id: genome
     type: select
     choices:
-      - [ 'refdata-cellranger-GRCh38-3.0.0', 'Human GRCh38 release 93']
-      - [ 'refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38 release 84']
-      - [ 'refdata-cellranger-hg19-3.0.0', 'Human GRCh37 (hg19) release 87']
-      - [ 'refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
-      - [ 'refdata-cellranger-mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
-      - [ 'refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
-      - [ 'refdata-cellranger-hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
-      - [ 'refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
-      - [ 'refdata-cellranger-ercc92-1.2.0', 'ERCC.92 Spike-In']
+      - [ 'GRCh38-3.0.0', 'Human GRCh38 release 93']
+      - [ 'GRCh38-1.2.0', 'Human GRCh38 release 84']
+      - [ 'hg19-3.0.0', 'Human GRCh37 (hg19) release 87']
+      - [ 'hg19-1.2.0', 'Human GRCh37 (hg19) release 84']
+      - [ 'mm10-3.0.0', 'Mouse GRCm38 (mm10) release 93']
+      - [ 'mm10-1.2.0', 'Mouse GRCm38 (mm10) release 84']
+      - [ 'hg19_and_mm10-3.0.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 93']
+      - [ 'hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19) release 84']
+      - [ 'ercc92-1.2.0', 'ERCC.92 Spike-In']
     required: true
     description: |
       Reference species and genome used for alignment and subsequent analysis.

workflow/conf/biohpc.config

@@ -18,6 +18,39 @@ process {
   }
 }
 
+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-'
+    }
+    '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-'
+    }
+  }
+}
+
 trace {
   enabled = true
   file = 'pipeline_trace.txt'

workflow/main.nf

@@ -6,7 +6,9 @@
 // Define Input variables
 params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'refdata-cellranger-GRCh38-1.2.0'
+params.genome = 'GRCh38-1.2.0'
+params.genomes = []
+params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
 params.expectCells = 10000
 params.forceCells = 0
 params.version = '3.0.2'
@@ -21,7 +23,7 @@ fastqList = Channel
   .map { file -> [ file.getFileName().toString(), file.toString() ].join("\t") }
   .collectFile(name: 'fileList.tsv', newLine: true)
 refLocation = Channel
-  .fromPath('/project/apps_database/cellranger/'+params.genome)
+  .fromPath(params.genomeLocation+params.genome)
   .ifEmpty { exit 1, "referene not found: ${params.genome}" }
 expectCells = params.expectCells
 forceCells = params.forceCells