From d42281a9ae6eacc907cab8106dd5cda11760271c Mon Sep 17 00:00:00 2001
From: Kai Waldrant <kai@data-intuitive.com>
Date: Mon, 5 Feb 2024 22:25:06 +0100
Subject: [PATCH] add script to call

---
 src/lofreq/call/config.vsh.yaml | 16 ++++-----
 src/lofreq/call/script.sh       | 58 +++++++++++++++++++++++++++++++++
 2 files changed, 65 insertions(+), 9 deletions(-)
 create mode 100644 src/lofreq/call/script.sh

diff --git a/src/lofreq/call/config.vsh.yaml b/src/lofreq/call/config.vsh.yaml
index 321681ab..d979c2b5 100644
--- a/src/lofreq/call/config.vsh.yaml
+++ b/src/lofreq/call/config.vsh.yaml
@@ -25,6 +25,13 @@ functionality:
             Input BAM file.
           required: true
           example: "normal.bam"
+        - name: --ref
+          alternatives: -f
+          type: file
+          description: |
+            Indexed reference fasta file (gzip supported) [null].
+          required: true
+          example: "reference.fasta"
     - name: Outputs
       arguments:
         - name: --output
@@ -37,13 +44,6 @@ functionality:
           example: "output.vcf"
     - name: Arguments
       arguments:
-        - name: --ref
-          alternatives: -f
-          type: file
-          description: |
-            Indexed reference fasta file (gzip supported) [null].
-          required: false
-          example: "reference.fasta"
         - name: --region
           alternatives: -r
           type: string
@@ -157,8 +157,6 @@ functionality:
           description: |
             Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by commas.
           required: false
-          multiple: true
-          separator: ","
           example: "variants.vcf"
         - name: --def_nm_q
           alternatives: -T
diff --git a/src/lofreq/call/script.sh b/src/lofreq/call/script.sh
new file mode 100644
index 00000000..39592c52
--- /dev/null
+++ b/src/lofreq/call/script.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+# Unset all parameters that are set to "false"
+[[ "$par_no_baq" == "false" ]] && unset par_no_baq
+[[ "$par_no_idaq" == "false" ]] && unset par_no_idaq
+[[ "$par_del_baq" == "false" ]] && unset par_del_baq
+[[ "$par_no_ext_baq" == "false" ]] && unset par_no_ext_baq
+[[ "$par_no_mq" == "false" ]] && unset par_no_mq
+[[ "$par_call_indels" == "false" ]] && unset par_call_indels
+[[ "$par_only_indels" == "false" ]] && unset par_only_indels
+[[ "$par_src_qual" == "false" ]] && unset par_src_qual
+[[ "$par_illumina_13" == "false" ]] && unset par_illumina_13
+[[ "$par_use_orphan" == "false" ]] && unset par_use_orphan
+[[ "$_plp_summary_only" == "false" ]] && unset _plp_summary_only
+[[ "$par_no_default_filter" == "false" ]] && unset par_no_default_filter
+[[ "$par_force_overwrite" == "false" ]] && unset par_force_overwrite
+[[ "$par_verbose" == "false" ]] && unset par_verbose
+[[ "$par_debug" == "false" ]] && unset par_debug
+
+# Run lofreq call
+lofreq call \
+  -f "$par_ref" \
+  -o "$par_output" \
+  ${par_region:+-r "${par_region}"} \
+  ${par_bed:+-l "${par_bed}"} \
+  ${par_min_bq:+-q "${par_min_bq}"} \
+  ${par_min_alt_bq:+-Q "${par_min_alt_bq}"} \
+  ${par_def_alt_bq:+-R "${par_def_alt_bq}"} \
+  ${par_min_jq:+-j "${par_min_jq}"} \
+  ${par_alt_jq:+-K "${par_alt_jq}"} \
+  ${par_no_baq:+-B} \
+  ${par_no_idaq:+-A} \
+  ${par_del_baq:+-D} \
+  ${par_no_ext_baq:+-e} \
+  ${par_min_mq:+-m "${par_min_mq}"} \
+  ${par_max_mq:+-M "${par_max_mq}"} \
+  ${par_no_mq:+-N} \
+  ${par_call_indels:+--call-indels} \
+  ${par_only_indels:+--only-indels} \
+  ${par_src_qual:+-s} \
+  ${par_ign_vcf:+-S "${par_ign_vcf}"} \
+  ${par_def_nm_q:+-T "${par_def_nm_q}"} \
+  ${par_sig:+-a "${par_sig}"} \
+  ${par_bonf:+-b "${par_bonf}"} \
+  ${par_min_cov:+-C "${par_min_cov}"} \
+  ${par_max_depth:+-d "${par_max_depth}"} \
+  ${par_illumina_13:+--illumina-1.3} \
+  ${par_use_orphan:+--use-orphan} \
+  ${par_plp_summary_only:+--plp-summary-only} \
+  ${par_no_default_filter:+--no-default-filter} \
+  ${par_force_overwrite:+--force-overwrite} \
+  ${par_verbose:+--verbose} \
+  ${par_debug:+--debug} \
+  "$par_input"
+