add dummy argument to samtools_fastq to share the script with samtool…

…s_fasta
emmarousseau · May 30, 2024 · 7d895a1 · 7d895a1
1 parent 8b708fb
commit 7d895a1
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 1 deletion.
diff --git 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
@@ -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} \