Merge branch '29-CountDesign' into 'develop'

Resolve "Fix CountDesign"

Closes #29

See merge request !44

.gitlab-ci.yml

@@ -25,11 +25,6 @@ astrocyte_check:
 
 simple_1FC:
   stage: simple
-  except:
-    changes:
-      - "**/*.md"
-    refs:
-      - tags
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple1/*.tar.gz" --designFile "test_data/simple1/cellranger-tiny-bcl-simple-1_2_0.csv"
     - pytest -m simple1
@@ -47,9 +42,6 @@ simple_1FC:
 
 simple_2FC:
   stage: simple
-  except:
-    changes:
-      - "**/*.md"
   script:
     - nextflow run workflow/main.nf --bcl "test_data/simple2/*.tar.gz" --designFile "test_data/simple2/cellranger-tiny-bcl-simple-1_2_0.csv"
     - pytest -m simple2

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
-* Add Except md to CI
 
 *Known Bugs*
 * cellranger mkfastq will not accept spaces in path for run param even if quoted, issue raised on 10XGenomics/cellranger github issue [#31](https://github.com/10XGenomics/cellranger/issues/31)

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;