From beeaae58732695c927907c61b566f3822f78196b Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Sat, 20 Jul 2024 15:49:16 +0200
Subject: [PATCH] Update src/umi_tools/umi_tools_extract/config.vsh.yaml

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 src/umi_tools/umi_tools_extract/config.vsh.yaml | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/umi_tools/umi_tools_extract/config.vsh.yaml b/src/umi_tools/umi_tools_extract/config.vsh.yaml
index 5eb8ac16..a980f149 100644
--- a/src/umi_tools/umi_tools_extract/config.vsh.yaml
+++ b/src/umi_tools/umi_tools_extract/config.vsh.yaml
@@ -17,17 +17,16 @@ argument_groups:
 
   - name: Input
     arguments: 
-    - name: --paired
-      type: boolean_true
-      description: Paired fastq files. If option is set, two input files are expected.
     - name: --input
       type: file
       required: true
-      description: Input fastq files, either one or two (paired).
+      description: File containing the input data.
       example: sample.fastq
     - name: --read2_in
       type: file
-      description: Filename for read pairs.
+      required: false
+      description: File containing the input data for the R2 reads (if paired). If provided, a <list of other required arguments> need to be provided.
+      example: sample_R2.fastq
     - name: --bc_pattern
       type: string
       description: |