diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh
index fb01295a..9c8a13ab 100644
--- a/src/fastqc/script.sh
+++ b/src/fastqc/script.sh
@@ -8,20 +8,27 @@
 [[ "$par_nano" == "false" ]] && unset par_nano
 [[ "$par_nofilter" == "false" ]] && unset par_nofilter
 [[ "$par_extract" == "false" ]] && unset par_extract
-#[[ -z "$par_java" ]] && unset par_java
 [[ "$par_noextract" == "false" ]] && unset par_noextract
 [[ "$par_nogroup" == "false" ]] && unset par_nogroup
-#[[ "$par_min_length" == "false" ]] && unset par_min_length
-#[[ "$par_format" == "false" ]] && unset par_format
-#[[ "$par_threads" == "false" ]] && unset par_threads
-#[[ "$par_contaminants" == "false" ]] && unset par_contaminants
-#[[ "$par_adapters" == "false" ]] && unset par_adapters
-#[[ "$par_limits" == "false" ]] && unset par_limits
-#[[ "$par_kmers" == "false" ]] && unset par_kmers
 [[ "$par_quiet" == "false" ]] && unset par_quiet
-#[[ "$par_dir" == "false" ]] && unset par_dir
 
-# run fastqc
+# if more than one file is passed
+if [[ "$par_input" == *","* ]]; then
+  
+  # Retrieve the first path from the comma-separated input
+  par_input1=$(echo "$par_input" | cut -d',' -f1)
+  # Retrieve the directory of the input file
+  input_dir=$(dirname "$par_input1")
+  # Convert comma to space separated
+  par_input=$(echo $par_input | tr ',' ' ')
+
+else # if only one file is passed
+  # Retrives the directory of the input file
+  input_dir=$(dirname "$par_input")
+fi
+echo "input_dir: $input_dir"
+
+run fastqc
 fastqc \
   ${par_outdir:+--outdir "$par_outdir"} \
   ${par_casava:+--casava} \
@@ -43,11 +50,6 @@ fastqc \
   $par_input
 
 
-# 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"
@@ -64,9 +66,23 @@ fi
 
 
 # Questions:
-# Should I unzip the zip file and make multiple other outputs for the viash component?
+# Should I unzip the zip file output and make multiple other outputs options for the viash component?
 # TODO: handle the output args if multiple files are passed
+# - if multiple files are passed, for the output args I can either change the config to multiple=false 
+# and pass just a dir as argument and mv the files to this dir, 
+# and would also work as well in the case of just one file passed (rename would be possible).
+# i guess I can discuss this with jakub and see what he thinks is best
+# because this is very similar to the -outdir flag!
+# Do I create a code for the multiple files case where I also rename the files to the output args?
 
 
 
-  
\ No newline at end of file
+#[[ -z "$par_java" ]] && unset par_java
+#[[ "$par_min_length" == "false" ]] && unset par_min_length
+#[[ "$par_format" == "false" ]] && unset par_format
+#[[ "$par_threads" == "false" ]] && unset par_threads
+#[[ "$par_contaminants" == "false" ]] && unset par_contaminants
+#[[ "$par_adapters" == "false" ]] && unset par_adapters
+#[[ "$par_limits" == "false" ]] && unset par_limits
+#[[ "$par_kmers" == "false" ]] && unset par_kmers
+#[[ "$par_dir" == "false" ]] && unset par_dir
\ No newline at end of file