script.sh

src/bcftools/bcftools_norm/config.vsh.yaml

@@ -103,7 +103,18 @@ argument_groups:
         alternatives: -N
         type: boolean_true
         description: Do not normalize indels (with -m or -c s).
-
+
+      - name: --output_type
+        alternatives: --O
+        type: string
+        choices: ['u', 'z', 'b', 'v']
+        description: | 
+          Output type:
+            u: uncompressed BCF
+            z: compressed VCF
+            b: compressed BCF
+            v: uncompressed VCF
+      
       - name: --old_rec_tag
         type: string
         description: Annotate modified records with INFO/STR indicating the original variant.

src/bcftools/bcftools_norm/script.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+    par_atomize
+    par_remove_duplicates
+    par_force
+    par_no_version
+    par_do_not_normalize
+    par_strict_filter
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Execute bcftools norm with the provided arguments
+bcftools norm \
+    ${par_atomize:+--atomize} \
+    ${par_atom_overlaps:+--atom-overlaps "$par_atom_overlaps"} \
+    ${par_check_ref:+--check-ref "$par_check_ref"} \
+    ${par_remove_duplicates:+--remove-duplicates} \
+    ${par_rm_dup:+--rm-dup "$par_rm_dup"} \
+    ${par_fasta_ref:+--fasta-ref "$par_fasta_ref"} \
+    ${par_force:+--force} \
+    ${par_keep_sum:+--keep-sum "$par_keep_sum"} \
+    ${par_multiallelics:+--multiallelics "$par_multiallelics"} \
+    ${par_no_version:+--no-version} \
+    ${par_do_not_normalize:+--do-not-normalize} \
+    ${par_old_rec_tag:+--old-rec-tag "$par_old_rec_tag"} \
+    ${par_regions:+--regions "$par_regions"} \
+    ${par_regions_file:+--regions-file "$par_regions_file"} \
+    ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \
+    ${par_site_win:+--site-win "$par_site_win"} \
+    ${par_strict_filter:+--strict-filter} \
+    ${par_targets:+--targets "$par_targets"} \
+    ${par_targets_file:+--targets-file "$par_targets_file"} \
+    ${par_targets_overlap:+--targets-overlap "$par_targets_overlap"} \
+    ${par_threads:+--threads "$par_threads"} \
+    ${par_output_type:+-O "$par_output_type"} \
+    -o $par_output \
+    $par_input
+