Merge branch '11-10x.kit.version' into 'develop'

Resolve "Add parameter for 10x kit version"

Closes #11

See merge request !12

astrocyte_pkg.yml

@@ -128,6 +128,17 @@ workflow_parameters:
     description: |
       Force pipeline to use this number of cells, bypassing the cell detection algorithm. Use this if the number of cells estimated by Cell Ranger is not consistent with the barcode rank plot. A value of 0 ignores this option. Any value other than 0 overrides expect-cells.
 
+  - id: kitVersion
+    type: select
+    default: 'auto'
+    choices:
+      - [ 'auto', 'Auto Detect']
+      - [ '3', '3']
+      - [ '2', '2']
+    required: true
+    description: |
+      10x single cell gene expression chemistry version (only used in cellranger version 2.x).
+
   - id: version
     type: select
     default: '3.0.2'
@@ -139,6 +150,7 @@ workflow_parameters:
     description: |
       10x cellranger version.
 
+
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------

workflow/conf/biohpc.config

@@ -52,6 +52,21 @@ params {
       loc = '/project/apps_database/cellranger/refdata-cellranger-'
     }
   }
+  // Chemistry mapping parameter
+  chemistry {
+    'auto' {
+      param = 'auto'
+    }
+    '1' {
+      param = 'SC3Pv1'
+    }
+   '2' {
+      param = 'SC3Pv2'
+    }
+   '3' {
+      param = 'SC3Pv3'
+    }
+  }
 }
 
 trace {

workflow/main.nf

@@ -6,11 +6,14 @@
 // Define Input variables
 params.fastq = "$baseDir/../test_data/*.fastq.gz"
 params.designFile = "$baseDir/../test_data/design.csv"
-params.genome = 'GRCh38-1.2.0'
+params.genome = 'GRCh38-3.0.0'
 params.genomes = []
 params.genomeLocation = params.genome ? params.genomes[ params.genome ].loc ?: false : false
 params.expectCells = 10000
 params.forceCells = 0
+params.kitVersion = '3'
+params.chemistry = []
+params.chemistryParam = params.kitVersion ? params.chemistry[ params.kitVersion ].param ?: false : false
 params.version = '3.0.2'
 params.outDir = "$baseDir/output"
 
@@ -28,6 +31,7 @@ refLocation = Channel
   .ifEmpty { exit 1, "referene not found: ${params.genome}" }
 expectCells = params.expectCells
 forceCells = params.forceCells
+chemistryParam = params.chemistryParam
 version = params.version
 outDir = params.outDir
 
@@ -69,13 +73,14 @@ refLocation.into {
   refLocation301
   refLocation302
 }
-
 expectCells211 = expectCells
 expectCells301 = expectCells
 expectCells302 = expectCells
 forceCells211 = forceCells
 forceCells301 = forceCells
 forceCells302 = forceCells
+chemistryParam301 = chemistryParam
+chemistryParam302 = chemistryParam
 
 process count211 {
   tag "count211-$sample"
@@ -119,6 +124,7 @@ process count301 {
   file ref from refLocation301.first()
   expectCells301
   forceCells301
+  chemistryParam301
 
   output:
 
@@ -130,11 +136,11 @@ process count301 {
   script:
   if (forceCells301 == 0){
     	"""
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
     	"""
   } else {
     	"""
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
     	"""
   }
 }
@@ -150,6 +156,7 @@ process count302 {
   file ref from refLocation302.first()
   expectCells302
   forceCells302
+  chemistryParam302
 
   output:
 
@@ -161,11 +168,11 @@ process count302 {
   script:
   if (forceCells302 == 0){
     	"""
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
     	"""
   } else {
     	"""
-    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
     	"""
   }
 }