Fix countDesign

CHANGELOG.md

 # v1.3.0 (in development)
 **User Facing**
 * Change Cellranger Version to 3.1.0
+* Fix countDesign to take multiple samples
 
 **Background**
 * Add CI artifacts

workflow/scripts/countDesign.sh

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