From f89e24a02e0eefee48e3221909f932030a612a81 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Fri, 19 Jul 2024 10:35:54 -0300
Subject: [PATCH] Update script.sh

---
 src/fastqc/script.sh | 33 ++++++++++++++++++++++++++++++++-
 1 file changed, 32 insertions(+), 1 deletion(-)

diff --git a/src/fastqc/script.sh b/src/fastqc/script.sh
index ca51b006..bae6644c 100644
--- a/src/fastqc/script.sh
+++ b/src/fastqc/script.sh
@@ -4,10 +4,41 @@
 ## VIASH END
 
 # unset flags
-[[ "$par_casava" == "false" ]] && unset par_
+[[ "$par_casava" == "false" ]] && unset par_casava
+[[ "$par_nano" == "false" ]] && unset par_nano
+[[ "$par_nofilter" == "false" ]] && unset par_nofilter
+[[ "$par_extract" == "false" ]] && unset par_extract
+[[ "$par_java" == "false" ]] && 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
 fastqc \
+  ${par_outdir:+--outdir "$par_outdir"} \
   ${par_casava:+--casava} \
+  ${par_nano:+--nano} \
+  ${par_nofilter:+--nofilter} \
+  ${par_extract:+--extract} \
+  ${par_java:+--java "$par_java"} \
+  ${par_noextract:+--noextract} \
+  ${par_nogroup:+--nogroup} \
+  ${par_min_length:+--min_length "$par_min_length"} \
+  ${par_format:+--format "$par_format"} \
+  ${par_threads:+--threads "$par_threads"} \
+  ${par_contaminants:+--contaminants "$par_contaminants"} \
+  ${par_adapters:+--adapters "$par_adapters"} \
+  ${par_limits:+--limits "$par_limits"} \
+  ${par_kmers:+--kmers "$par_kmers"} \
+  ${par_quiet:+--quiet} \
+  ${par_dir:+--dir "$par_dir"} \
   $par_input
   
\ No newline at end of file