Extra arg to allow use of bbmap args

viash-hub · Sep 23, 2024 · 82bd7b8 · 82bd7b8
1 parent d6c3fb4
commit 82bd7b8
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/src/bbmap_bbsplit/config.vsh.yaml b/src/bbmap_bbsplit/config.vsh.yaml
@@ -130,7 +130,11 @@ argument_groups:
   - name: "--nzo"
     type: boolean_true
     description: Only print lines with nonzero coverage.
-
+  - name: "--bbmap_args"
+    type: string
+    description: |
+      Additional arguments from BBMap to pass to BBSplit.
+    
 resources:
   - type: bash_script
     path: script.sh

diff --git a/src/bbmap_bbsplit/script.sh b/src/bbmap_bbsplit/script.sh
@@ -63,6 +63,9 @@ else
     if [ "$par_untrim" = true ]; then extra_args+=" --untrim"; fi
     if [ "$par_nzo" = true ]; then extra_args+=" --nzo"; fi
 
+    if [ -n "$par_bbmap_args" ]; then extra_args+=" $par_bbmap_args"; fi
+
+
     if $par_paired; then
         bbsplit.sh \
             $index_files \