Resolve "update check design file"

Closes #13 (closed)

workflow/main.nf

@@ -15,6 +15,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
 params.tssFile = params.genome ? params.genomes[ params.genome ].tssfile ?: false : false
+params.astrocyte = false
 params.outDir= "${baseDir}/output"
 
 // Check inputs
@@ -40,6 +41,7 @@ tn5 = params.tn5
 designFile = params.designFile
 genomeSize = params.genomeSize
 chromSizes = params.chromSizes
+outDir = params.outDir
 //tssFile = params.tssFile
 
 process checkDesignFile {
@@ -54,15 +56,31 @@ process checkDesignFile {
     file("design.tsv") into designFilePaths
 
   script:
-    if (pairedEnd) {
-      """
-      python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
-      """
+    if (params.astrocyte == true) {
+      if (pairedEnd) {
+        """
+        module load python/3.6.1-2-anaconda
+        python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
+        """
+      }
+      else {
+        """
+        module load python/3.6.1-2-anaconda
+        python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
+        """
+      }
     }
     else {
-      """
-      python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
-      """
+      if (pairedEnd) {
+        """
+        python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -p -a
+        """
+      }
+      else {
+        """
+        python3 ${baseDir}/scripts/check_design.py -d ${designFile} -f ${readsList} -a
+        """
+      }
     }
 
 }