Resolve "Move module load into nextflow process"

Closes #26 (closed) Moved to Bash Script

workflow/main.nf

@@ -130,12 +130,40 @@ process count211 {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells211
     """
   } else {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells211
     """
   }
@@ -167,12 +195,40 @@ process count301 {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells301 --chemistry="$chemistryParam301"
     """
   } else {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells301 --chemistry="$chemistryParam301"
     """
   }
@@ -204,12 +260,40 @@ process count302 {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --expect-cells=$expectCells302 --chemistry="$chemistryParam302"
     """
   } else {
     """
 	  hostname
     ulimit -a
+
+    name=`readlink -e $ref`
+    if [ `find \$name -name "* *" | wc -l` -gt 0 ]
+    then echo "Error: Spaces found in Reference Files"
+    echo `find \$name -name "* *"`
+    exit 2
+    fi
+
+    if [ \$(echo "$ref" | tr -d ' ') != "$ref" ]
+    then echo "Error: Spaces found in Reference Files"
+    echo "$ref"
+    exit 2 
+    fi
+
     cellranger count --id="$sample" --transcriptome="./$ref" --fastqs=. --sample="$sample" --force-cells=$forceCells302 --chemistry="$chemistryParam302"
     """
   }