From 2e5e79721d06a0df107e9f45d06b9ec612301764 Mon Sep 17 00:00:00 2001
From: tgaspe <theodorogtc@gmail.com>
Date: Thu, 29 Aug 2024 15:08:12 +0200
Subject: [PATCH] Update script.sh

---
 src/bcftools/bcftools_concat/script.sh | 46 ++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)

diff --git a/src/bcftools/bcftools_concat/script.sh b/src/bcftools/bcftools_concat/script.sh
index e69de29b..6cd9d4db 100644
--- a/src/bcftools/bcftools_concat/script.sh
+++ b/src/bcftools/bcftools_concat/script.sh
@@ -0,0 +1,46 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+    par_allow_overlaps
+    par_compact_PS
+    par_ligate
+    par_ligate_force
+    par_ligate_warn
+    par_no_version
+    par_naive
+    par_naive_force
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Execute bcftools concat with the provided arguments
+bcftools concat \
+    ${par_allow_overlaps:+-a} \
+    ${par_compact_PS:+-c} \
+    ${par_remove_duplicates:+-d "$par_remove_duplicates"} \
+    ${par_file_list:+-f "$par_file_list"} \
+    ${par_ligate:+-l} \
+    ${par_ligate_force:+--ligate-force} \
+    ${par_ligate_warn:+--ligate-warn} \
+    ${par_no_version:+--no-version} \
+    ${par_naive:+-n} \
+    ${par_naive_force:+--naive-force} \
+    ${par_output_type:+--O "$par_output_type"} \
+    ${par_min_PQ:+-q "$par_min_PQ"} \
+    ${par_regions:+-r "$par_regions"} \
+    ${par_regions_file:+-R "$par_regions_file"} \
+    ${par_regions_overlap:+--regions-overlap "$par_regions_overlap"} \
+    ${par_threads:+--threads "$par_threads"} \
+    ${par_verbose:+-v "$par_verbose"} \
+    -o $par_output \
+    $par_input
\ No newline at end of file