Hardwire ref genome locations into astrocyte yml

astrocyte_pkg.yml

@@ -95,11 +95,11 @@ workflow_parameters:
   - id: genome
     type: select
     choices:
-      - [ 'GRCh38', 'Human GRCh38']
-      - [ 'hg19', 'Human GRCh37 (hg19)']
-      - [ 'mm10', 'Mouse GRCm38 (mm10)']
-      - [ 'hg19.mm10', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
-      - [ 'ercc92', 'ERCC.92 Spike-In']
+      - [ '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0', 'Human GRCh38']
+      - [ '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0', 'Human GRCh37 (hg19)']
+      - [ '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0', 'Mouse GRCm38 (mm10)']
+      - [ '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0', 'Human GRCh37 (hg19) + Mouse GRCm38 (mm19)']
+      - [ '/project/apps_database/cellranger/refdata-cellranger-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

@@ -12,27 +12,6 @@ process {
   }
 }
 
-params {
-  // Reference file paths on BioHPC
-  genomes {
-    'ercc92' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-ercc92-1.2.0'
-    }
-    'GRCh38' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
-    }
-    'hg19' {
-	ref = '/project/apps_database/cellranger/refdata-cellranger-hg19-1.2.0'
-    }
-    'mm10' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-mm10-1.2.0'
-    }
-    'hg19.mm10' {
-      ref = '/project/apps_database/cellranger/refdata-cellranger-hg19_and_mm10-1.2.0'
-    }
-  }
-}
-
 trace {
   enabled = true
   file = 'pipeline_trace.txt'

workflow/main.nf

@@ -6,25 +6,10 @@
 // Define Input variables
 params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'GRCh38'
-params.genomes = []
-params.ref = params.genome ? params.genomes[ params.genome ].ref ?: false : false
+params.genome = '/project/apps_database/cellranger/refdata-cellranger-GRCh38-1.2.0'
 params.expectCells = 10000
 params.forceCells = 0
 
-println params.genome
-println params.genomes[ params.genome ].ref
-println params.ref
-
-// Check inputs
-if( params.ref ){
-  refLocation = Channel
-    .fromPath(params.ref)
-    .ifEmpty { exit 1, "referene not found: ${params.ref}" }
-} else {
-  exit 1, "No reference genome specified."
-}
-
 // Define List of Files
 fastqList = Channel
   .fromPath(params.fastq)
@@ -33,6 +18,9 @@ fastqList = Channel
   .collectFile(name: 'fileList.tsv', newLine: true)
 
 // Define regular variables
+refLocation = Channel
+  .fromPath(params.genome)
+  .ifEmpty { exit 1, "referene not found: ${params.genome}" }
 expectCells = params.expectCells
 forceCells = params.forceCells