.gitignore

@@ -301,6 +301,7 @@ $RECYCLE.BIN/
 /workflow/work/*
 /workflow/output/*
 /.nextflow/*
+/data/*
 /work/*
 /output/*
 pipeline_trace*.txt*

astrocyte_pkg.yml

@@ -152,9 +152,9 @@ workflow_parameters:
 
   - id: astrocyte
     type: string
-    required: true
     default: 'true'
-    regex: "true"
+    required: true
+    regex: 'true'
     description: |
       Ensure configuraton for astrocyte.
 

workflow/conf/biohpc.config

@@ -9,15 +9,15 @@ process {
   }
   $count211 {
     module = ['cellranger/2.1.1']
-    memory = '120GB'
+    queue = '128GB,256GB,256GBv1,384GB'
   }
   $count301 {
     module = ['cellranger/3.0.1']
-    memory = '120GB'
+    queue = '128GB,256GB,256GBv1,384GB'
   }
   $count302 {
     module = ['cellranger/3.0.2']
-    memory = '120GB'
+    queue = '128GB,256GB,256GBv1,384GB'
   }
 }
 

workflow/main.nf

@@ -71,6 +71,8 @@ process checkDesignFile {
   script:
 
   """
+  hostname
+  ulimit -a
   module load python/3.6.1-2-anaconda
   python3 $baseDir/scripts/check_design.py -d $designLocation -f $fastqList
   """
@@ -104,7 +106,7 @@ chemistryParam301 = chemistryParam
 chemistryParam302 = chemistryParam
 
 process count211 {
-  memory  '120 GB'
+  queue '128GB,256GB,256GBv1,384GB'
   tag "count211-$sample"
 
   publishDir "$outDir/${task.process}", mode: 'copy'
@@ -129,17 +131,21 @@ process count211 {
   """
   if (forceCells211 == 0){
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
     	"""
   } else {
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
     	"""
   }
 }
 
 process count301 {
-  memory  '120 GB'
+  queue '128GB,256GB,256GBv1,384GB'
   tag "count301-$sample"
 
   publishDir "$outDir/${task.process}", mode: 'copy'
@@ -165,17 +171,21 @@ process count301 {
   """
   if (forceCells301 == 0){
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
     	"""
   } else {
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
     	"""
   }
 }
 
 process count302 {
-  memory  '120 GB'
+  queue '128GB,256GB,256GBv1,384GB'
   tag "count302-$sample"
 
   publishDir "$outDir/${task.process}", mode: 'copy'
@@ -201,10 +211,14 @@ process count302 {
   """
   if (forceCells302 == 0){
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
     	"""
   } else {
     	"""
+	hostname
+    	ulimit -a
     	cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
     	"""
   }