From fb3a18e5e888f9ecd6fbec5a88c9df83c3181275 Mon Sep 17 00:00:00 2001
From: "lotte.pronk" <74367992+LottePronk@users.noreply.github.com>
Date: Fri, 17 Feb 2023 14:48:13 +0100
Subject: [PATCH] -gff instead of --prodigal_file in example of command line
 options

---
 README.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 30a512f..ed02b00 100644
--- a/README.md
+++ b/README.md
@@ -64,8 +64,7 @@ Use `whokaryote.py --help` to see all the options:
 -h, --help            show this help message and exit
 --contigs CONTIGS     The path to your contigs file. It should be one (multi)fasta (DNA).
 --outdir OUTDIR       Specify the path to your preferred output directory. No / at the end.
---prodigal_file PRODIGAL_FILE
-                        If you already have prodigal gene predictions, specify path to the .genes or .gff file
+--gff GFF             If you already have gene predictions, specify path to the .gff file"
 --f                   If you want new multifastas with only eukaryotes and only prokaryotes. This can take a long time.
 --minsize MINSIZE     Select a minimum contig size in bp, default = 5000. Accuracy on contigs below 5000 is lower.
 --model MODEL         Choose the stand-alone model or the tiara-integrated model: S or T. Option 'T' only works with argument --contigs