Update script.sh

src/bcftools/bcftools_annotate/script.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Exit on error
+set -eo pipefail
+
+# Unset parameters
+unset_if_false=(
+
+)
+
+for par in ${unset_if_false[@]}; do
+    test_val="${!par}"
+    [[ "$test_val" == "false" ]] && unset $par
+done
+
+# Create input array 
+IFS=";" read -ra input <<< $par_input
+
+# Execute bcftools annotate with the provided arguments
+bcftools annotate \
+    ${par_first_allele_only:+--1st-allele-only} \
+    ${par_split_by_ID:+--split-by-ID} \
+    ${par_verbose:+--verbose} \
+    ${par_allele_frequency_bins:+--af-bins "${par_allele_frequency_bins}"} \
+    ${par_allele_frequency_tag:+--af-tag "${par_allele_frequency_tag}"} \
+    ${par_collapse:+-c "${par_collapse}"} \
+    ${par_depth:+-d "${par_depth}"} \
+    ${par_exclude:+-e "${par_exclude}"} \
+    ${par_exons:+-E "${par_exons}"} \
+    ${par_apply_filters:+-f "${par_apply_filters}"} \
+    ${par_fasta_reference:+-F "${par_fasta_reference}"} \
+    ${par_include:+-i "${par_include}"} \
+    ${par_regions:+-r "${par_regions}"} \
+    ${par_regions_file:+-R "${par_regions_file}"} \
+    ${par_regions_overlap:+--regions-overlap "${par_regions_overlap}"} \
+    ${par_samples:+-s "${par_samples}"} \
+    ${par_samples_file:+-S "${par_samples_file}"} \
+    ${par_targets:+-t "${par_targets}"} \
+    ${par_targets_file:+-T "${par_targets_file}"} \
+    ${par_targets_overlaps:+--targets-overlap "${par_targets_overlaps}"} \
+    ${par_user_tstv:+-u "${par_user_tstv}"} \
+    "${input[@]}" \
+    > $par_output