From 237a2e3a229ee589d1ebbc282526f87398e26f58 Mon Sep 17 00:00:00 2001
From: Hendrik Cannoodt <hendrik.cannoodt@gmail.com>
Date: Fri, 27 Sep 2024 11:52:08 +0200
Subject: [PATCH] Fixes the typo raised in issue #132 (#157)

* Fixes the typo raised in issue #132

* Add changelog entry

* fix typo, modify script

---------

Co-authored-by: jakubmajercik <jakub.majercik@gmail.com>
---
 CHANGELOG.md              | 4 ++++
 src/falco/config.vsh.yaml | 2 +-
 src/falco/script.sh       | 4 ++--
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0613fa25..a2aa5387 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,10 @@
 
 * `rsem/rsem_calculate_expression`: Calculate expression levels (PR #93).
 
+## BREAKING CHANGES
+
+* `falco`: Fix a typo in the `--reverse_complement` argument (PR #157).
+
 ## MINOR CHANGES
 
 * Upgrade to Viash 0.9.0.
diff --git a/src/falco/config.vsh.yaml b/src/falco/config.vsh.yaml
index de9906ef..a161e252 100644
--- a/src/falco/config.vsh.yaml
+++ b/src/falco/config.vsh.yaml
@@ -86,7 +86,7 @@ argument_groups:
           bisulfite sequencing, and more Ts and fewer 
           Cs are therefore expected and will be 
           accounted for in base content.
-      - name: --reverse_complliment
+      - name: --reverse_complement
         alternatives: [-r]
         type: boolean_true
         description: |
diff --git a/src/falco/script.sh b/src/falco/script.sh
index 43f5efe5..13e2eab4 100644
--- a/src/falco/script.sh
+++ b/src/falco/script.sh
@@ -4,7 +4,7 @@ set -eo pipefail
 
 [[ "$par_nogroup" == "false" ]] && unset par_nogroup
 [[ "$par_bisulfite" == "false" ]] && unset par_bisulfite
-[[ "$par_reverse_compliment" == "false" ]] && unset par_reverse_compliment
+[[ "$par_reverse_complement" == "false" ]] && unset par_reverse_complement
 
 IFS=";" read -ra input <<< $par_input
 
@@ -15,7 +15,7 @@ $(which falco) \
   ${par_limits:+--limits "$par_limits"} \
   ${par_subsample:+-subsample $par_subsample} \
   ${par_bisulfite:+-bisulfite} \
-  ${par_reverse_compliment:+-reverse-compliment} \
+  ${par_reverse_complement:+-reverse-complement} \
   ${par_outdir:+--outdir "$par_outdir"} \
   ${par_format:+--format "$par_format"} \
   ${par_data_filename:+-data-filename "$par_data_filename"} \