From 72c3ab9a66f01ebfaf17a43ff1472bf70474dc13 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Fri, 19 Jul 2024 16:45:33 -0300
Subject: [PATCH] trying to figure multiple: true

---
 src/fastqc/config.vsh.yaml                    | 5 ++++-
 src/fastqc/script.sh                          | 2 ++
 src/fastqc/test.sh                            | 3 +++
 src/fastqc/test_data/{input.fq => input_1.fq} | 0
 src/fastqc/test_data/input_2.fq               | 4 ++++
 5 files changed, 13 insertions(+), 1 deletion(-)
 rename src/fastqc/test_data/{input.fq => input_1.fq} (100%)
 create mode 100644 src/fastqc/test_data/input_2.fq

diff --git a/src/fastqc/config.vsh.yaml b/src/fastqc/config.vsh.yaml
index 0b36e46c..c84f9008 100644
--- a/src/fastqc/config.vsh.yaml
+++ b/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
         
@@ -25,6 +26,7 @@ argument_groups:
       - name: --html
         type: file
         direction: output
+        multiple: true
         description: |
           Create an HTML report of the results.
         example: report_fastqc.html
@@ -32,6 +34,7 @@ argument_groups:
       - name: --zip
         type: file
         direction: output
+        multiple: true
         description: |
           Create an zip file with: html report, data, images, icons etc.
         example: report_fastqc.html
diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh
index 0c82a929..fb01295a 100644
--- a/src/fastqc/script.sh
+++ b/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"
diff --git a/src/fastqc/test.sh b/src/fastqc/test.sh
index 25461fd8..73fd9bb9 100644
--- a/src/fastqc/test.sh
+++ b/src/fastqc/test.sh
@@ -20,3 +20,6 @@ CACTTGTAAGGGCAGGCCCCCTTCACCCTCCCGCTCCTGGGGGANNNNNNNNNNANNNCGAGGCCCTGGGGTAGAGGGNN
 @?@DDDDDDHHH?GH:?FCBGGB@C?DBEGIIIIAEF;FCGGI#########################################################
 EOL
 
+# Test 1: Run fastqc with default parameters
+
+
diff --git a/src/fastqc/test_data/input.fq b/src/fastqc/test_data/input_1.fq
similarity index 100%
rename from src/fastqc/test_data/input.fq
rename to src/fastqc/test_data/input_1.fq
diff --git a/src/fastqc/test_data/input_2.fq b/src/fastqc/test_data/input_2.fq
new file mode 100644
index 00000000..941c563e
--- /dev/null
+++ b/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#########################################################
\ No newline at end of file