Merge branch '1-cellranger3.0.1' into 'develop'

Resolve "Add cellranger v3.0.1"

Closes #1

See merge request !2

astrocyte_pkg.yml

@@ -41,6 +41,7 @@ documentation_files:
 workflow_modules:
   - 'python/3.6.1-2-anaconda'
   - 'cellranger/2.1.1'
+  - 'cellranger/3.0.1'
   - 'bcl2fastq/2.17.1.14'
 
 # A list of parameters used by the workflow, defining how to present them,
@@ -122,6 +123,16 @@ 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: version
+    type: select
+    default: 3.0.1
+    choices:
+      - [ 3, '3.0.1']
+      - [ 2, '2.0.1']
+    required: true
+    description: |
+      10x cellranger version.
+
 # -----------------------------------------------------------------------------
 # SHINY APP CONFIGURATION
 # -----------------------------------------------------------------------------

test_data/design.csv

-Sample,fastq_R1,fastq_R2
-D17PrPzF_BE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L001_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L001_R2_001.fastq.gz
-D17PrPzF_BE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L002_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_BE_S1_L002_R2_001.fastq.gz
-D17PrPzF_LE,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_LE_S3_L001_R1_001.fastq.gz,/work/urology/ghenry/Grimoire/Astrocyte/cellranger_count/test_data/D17PrPzF_LE_S3_L001_R2_001.fastq.gz
+Sample,fastq_R1,fastq_R2
+D17PrPzF_BE,D17PrPzF_BE_S1_L001_R1_001.fastq.gz,D17PrPzF_BE_S1_L001_R2_001.fastq.gz
+D17PrPzF_BE,D17PrPzF_BE_S1_L002_R1_001.fastq.gz,D17PrPzF_BE_S1_L002_R2_001.fastq.gz
+D17PrPzF_LE,D17PrPzF_LE_S3_L001_R1_001.fastq.gz,D17PrPzF_LE_S3_L001_R2_001.fastq.gz

workflow/conf/biohpc.config

@@ -7,9 +7,12 @@ process {
     module = ['python/3.6.1-2-anaconda']
     executor = 'local'
   }
-  $count {
+  $count2 {
     module = ['cellranger/2.1.1']
   }
+  $count3 {
+    module = ['cellranger/3.0.1']
+  }
 }
 
 trace {

workflow/main.nf

@@ -41,7 +41,6 @@ process checkDesignFile {
   script:
 
   """
-  module load python/3.6.1-2-anaconda
   python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
   """
 }
@@ -53,33 +52,78 @@ samples = designPaths
   .groupTuple()
   //.subscribe { println it }
 
+// Duplicate variables
+samples.into {
+  samples2
+  samples3
+}
+refLocation.into {
+  refLocation2
+  refLocation3
+}
+expectCells2 = expectCells
+expectCells3 = expectCells
+forceCells2 = forceCells
+forceCells3 = forceCells
+
+process count2 {
+  tag "count2-$sample"
+
+  publishDir "$baseDir/output", mode: 'copy'
+
+  input:
+
+  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples2
+  file ref from refLocation2.first()
+  expectCells2
+  forceCells2
+
+  output:
+
+  file("**/outs/**") into outPaths2
 
-process count {
-  tag "$sample"
+  when:
+  version == 2
+
+  script:
+  if (forceCells2 == 0){
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells2
+    	"""
+  } else {
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells2
+    	"""
+  }
+}
+
+process count3 {
+  tag "count3-$sample"
 
   publishDir "$baseDir/output", mode: 'copy'
 
   input:
 
-  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples
-  file ref from refLocation.first()
-  expectCells
-  forceCells
+  set sample, file("${sample}_S1_L00?_R1_001.fastq.gz"), file("${sample}_S1_L00?_R2_001.fastq.gz") from samples3
+  file ref from refLocation3.first()
+  expectCells3
+  forceCells3
 
   output:
 
-  file("**/outs/**") into outPaths
+  file("**/outs/**") into outPaths3
+
+  when:
+  version == 3
 
   script:
-  if (forceCells == 0){
-    """
-    module load cellranger/2.1.1
-    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells
-    """
+  if (forceCells3 == 0){
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells3
+    	"""
   } else {
-    """
-    module load cellranger/2.1.1
-    cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells
-    """
+    	"""
+    	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells3
+    	"""
   }
 }