Merge branch '26-ModuleLoad' into 'develop'

Resolve "Move module load into nextflow process"

Closes #26

See merge request !43

workflow/main.nf

@@ -130,12 +130,14 @@ process count211 {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
     """
   } else {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
     """
   }
@@ -167,12 +169,14 @@ process count301 {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
     """
   } else {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
     """
   }
@@ -204,12 +208,14 @@ process count302 {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
     """
   } else {
     """
 	  hostname
     ulimit -a
+    bash "$baseDir/scripts/filename_check.sh" -r "$ref"
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
     """
   }

workflow/scripts/filename_check.sh

+#!/bin/bash
+#filename_check.sh
+
+usage() {
+  echo "-r  --ref file"
+  exit 1
+}
+OPTIND=1
+while getopts :r: opt
+do
+   case $opt in
+        r) ref=$OPTARG;;
+   esac
+done
+
+shift $(($OPTIND -1));
+
+name=`readlink -e $ref`
+
+if [ `find $name -name "* *" | wc -l` -gt 0 ];
+then
+   echo "Error: Spaces found in Reference Files";
+   echo `find $name -name "* *"`;
+   exit 21;
+fi;
+
+if [ $(echo "$ref" | tr -d ' ') != "$ref" ];
+then
+   echo "Error: Spaces found in Reference Files";
+   echo "$ref";
+   exit 21;
+fi;