Merge branch '8-CountDesignFile' into 'develop'

Create Design file for count with 1 bcl input

Closes #8

See merge request !38

workflow/main.nf

@@ -13,6 +13,9 @@ params.references = "$baseDir/../docs/references.md"
 
 // Define List of Files
 tarList = Channel.fromPath( params.bcl )
+bclCount = Channel
+	.fromPath( params.bcl )
+	.count()
 
 // Define regular variables
 name = params.name
@@ -33,6 +36,7 @@ process checkDesignFile {
 
   output:
   file("design.checked.csv") into designPaths
+  file("design.checked.csv") into designCount
 
   script:
   """
@@ -74,6 +78,7 @@ process mkfastq {
 
   output:
   file("**/outs/**/*.fastq.gz") into fastqPaths
+  file("**/outs/**/*.fastq.gz") into cellrangerCount
   file("**/outs/fastq_path/Stats/Stats.json") into bqcPaths
   val "${bcl.baseName}" into bclName
 
@@ -85,6 +90,25 @@ process mkfastq {
   """
 }
 
+if (bclCount.value == 1) {
+  process countDesign {
+    tag "$name"
+    publishDir "$outDir/misc/${task.process}/$name", mode: 'copy'
+
+    input:
+    file fastqs from cellrangerCount.collect()
+    file design from designCount
+
+    output:
+    file("Cellranger_Count_Design.csv") into CountDesign
+
+    script:
+    """
+    bash "$baseDir/scripts/countDesign.sh"
+    """
+  }
+}
+
 process fastqc {
   tag "$bclName"
   queue 'super'

workflow/scripts/countDesign.sh

+#!/bin/bash
+#countDesign.sh
+
+fastqs=`ls *.fastq.gz`;
+design=`ls *.csv`;
+sample=`cat $design | tail -n +2 | cut -d ',' -f2`;
+
+for i in ${fastqs};
+do
+   if [[ ${i} == *_S0_* ]];
+   then
+	continue;
+   elif [[ ${i} == *_I* ]];
+   then
+	continue;
+   else
+	good=( "${good[@]}" "${i}" );
+   fi;
+done
+
+echo "Sample,fastq_R1,fastq_R2" > Cellranger_Count_Design.csv;
+echo "${sample},${good[0]},${good[1]}" >> Cellranger_Count_Design.csv;