trying to figure multiple: true

src/fastqc/config.vsh.yaml

@@ -16,7 +16,8 @@ argument_groups:
         type: file
         direction: input
         multiple: true
-        description: 
+        multiple_sep: ","
+        description: FASTQ file(s) to be analyzed.
         required: true
         example: input.fq
 
@@ -25,13 +26,15 @@ argument_groups:
       - name: --html
         type: file
         direction: output
+        multiple: true
         description: |
           Create an HTML report of the results.
         example: report_fastqc.html
 
       - name: --zip
         type: file
         direction: output
+        multiple: true
         description: |
           Create an zip file with: html report, data, images, icons etc.
         example: report_fastqc.html

src/fastqc/script.sh

@@ -46,6 +46,8 @@ fastqc \
 # Retrives the directory of the input file
 input_dir=$(dirname "$par_input")
 
+#echo "input is: $par_input"
+
 # Both outputs args passed
 if [[ -n "$par_html" ]] && [[ -n "$par_zip" ]]; then
   mv "$input_dir"/*.html "$par_html"

src/fastqc/test.sh

@@ -20,3 +20,6 @@ CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNN
 @?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################
 EOL
 
+# Test 1: Run fastqc with default parameters
+
+

src/fastqc/test_data/input_2.fq

@@ -0,0 +1,4 @@
+@HWI-ST330:304:H045HADXX:1:1101:1111:61397
+CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNNNNNNNNNNNNNNGATCTTGG
++
+@?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################