update multiple separator (#81)

* update multiple separator * update changelog * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * update ifs --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
viash-hub · Jul 11, 2024 · f71ed87 · f71ed87
1 parent 508a40a
commit f71ed87
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,8 @@
 
 * `cutadapt`: demultiplexing is now disabled by default. It can be re-enabled by using `demultiplex_mode`.
 
+* `multiqc`: update multiple separator to `;` (PR #81).
+
 ## MINOR CHANGES
 
 * `busco` components: update BUSCO to `5.7.1`.

diff --git a/src/multiqc/config.vsh.yaml b/src/multiqc/config.vsh.yaml
@@ -54,25 +54,21 @@ argument_groups:
       - name: "--include_modules"
         type: string
         multiple: true
-        multiple_sep: ","
-        example: fastqc,cutadapt
+        example: [fastqc, cutadapt]
         description: Use only these module
       - name: "--exclude_modules"
         type: string
         multiple: true
-        multiple_sep: ","
-        example: fastqc,cutadapt
+        example: [fastqc, cutadapt]
         description: Do not use only these modules
       - name: "--ignore_analysis"
         type: string
         multiple: true
-        multiple_sep: ","
-        example: run_one/*,run_two/*
+        example: [run_one/*, run_two/*]
       - name: "--ignore_samples"
         type: string
         multiple: true
-        multiple_sep: ","
-        example: sample_1*,sample_3*
+        example: [sample_1*, sample_3*]
       - name: "--ignore_symlinks"
         type: boolean_true
         description: Ignore symlinked directories and files

diff --git a/src/multiqc/script.sh b/src/multiqc/script.sh
@@ -38,7 +38,7 @@ IFS=";" read -ra inputs <<< $par_input
 
 if [[ -n "$par_include_modules" ]]; then
     include_modules=""
-    IFS="," read -ra incl_modules <<< $par_include_modules
+    IFS=";" read -ra incl_modules <<< $par_include_modules
     for i in "${incl_modules[@]}"; do
         include_modules+="--include $i "
     done
@@ -47,7 +47,7 @@ fi
 
 if [[ -n "$par_exclude_modules" ]]; then
     exclude_modules=""
-    IFS="," read -ra excl_modules <<< $par_exclude_modules
+    IFS=";" read -ra excl_modules <<< $par_exclude_modules
     for i in "${excl_modules[@]}"; do
         exclude_modules+="--exclude $i"
     done
@@ -56,7 +56,7 @@ fi
 
 if [[ -n "$par_ignore_analysis" ]]; then
     ignore=""
-    IFS="," read -ra ignore_analysis <<< $par_ignore_analysis
+    IFS=";" read -ra ignore_analysis <<< $par_ignore_analysis
     for i in "${ignore_analysis[@]}"; do
         ignore+="--ignore $i "
     done
@@ -65,7 +65,7 @@ fi
 
 if [[ -n "$par_ignore_samples" ]]; then
     ignore_samples=""
-    IFS="," read -ra ign_samples <<< $par_ignore_samples
+    IFS=";" read -ra ign_samples <<< $par_ignore_samples
     for i in "${ign_samples[@]}"; do
         ignore_samples+="--ignore-samples $i"
     done