From 7d895a104b90ecc7b9fd4a634530c9aed5f55d14 Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Thu, 30 May 2024 08:53:42 +0100
Subject: [PATCH] add dummy argument to samtools_fastq to share the script with
 samtools_fasta

---
 src/samtools/samtools_fastq/config.vsh.yaml | 5 +++++
 src/samtools/samtools_fastq/script.sh       | 2 +-
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/samtools/samtools_fastq/config.vsh.yaml b/src/samtools/samtools_fastq/config.vsh.yaml
index 39e926f0..39c11c49 100644
--- a/src/samtools/samtools_fastq/config.vsh.yaml
+++ b/src/samtools/samtools_fastq/config.vsh.yaml
@@ -26,6 +26,11 @@ argument_groups:
         direction: output
   - name: Options
     arguments:
+      - name: --command
+        type: string
+        description: |
+          This is a dummy argument to use the same script for multiple samtools commands.
+        default: fastq
       - name: --no_suffix
         alternatives: -n
         type: boolean_true
diff --git a/src/samtools/samtools_fastq/script.sh b/src/samtools/samtools_fastq/script.sh
index 367432f9..40949856 100644
--- a/src/samtools/samtools_fastq/script.sh
+++ b/src/samtools/samtools_fastq/script.sh
@@ -11,7 +11,7 @@ set -e
 [[ "$par_copy_tags" == "false" ]] && unset par_copy_tags
 [[ "$par_casava" == "false" ]] && unset par_casava
 
-samtools fastq \
+samtools "$par_command" \
     ${par_no_suffix:+-n} \
     ${par_suffix:+-N} \
     ${par_use_oq:+-O} \