From 535975eb81c9e48eb0403c136b7f1dd7acb1afad Mon Sep 17 00:00:00 2001
From: SusiJo <43847534+SusiJo@users.noreply.github.com>
Date: Fri, 15 Jul 2022 20:55:59 +0200
Subject: [PATCH] Update bcftools/stats for WES (#1893)

update bcftools/stats
---
 modules/bcftools/stats/main.nf       | 8 +++++++-
 modules/bcftools/stats/meta.yml      | 5 +++++
 tests/modules/bcftools/stats/main.nf | 4 ++--
 3 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/modules/bcftools/stats/main.nf b/modules/bcftools/stats/main.nf
index 1e0f3a47..c42ed29a 100644
--- a/modules/bcftools/stats/main.nf
+++ b/modules/bcftools/stats/main.nf
@@ -9,6 +9,7 @@ process BCFTOOLS_STATS {
 
     input:
     tuple val(meta), path(vcf)
+    path(target_bed)
 
     output:
     tuple val(meta), path("*stats.txt"), emit: stats
@@ -20,8 +21,13 @@ process BCFTOOLS_STATS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def target = target_bed ? "--regions-file ${target_bed}" : ""
     """
-    bcftools stats $args $vcf > ${prefix}.bcftools_stats.txt
+    bcftools stats \\
+        $args \\
+        $target \\
+        $vcf > ${prefix}.bcftools_stats.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
diff --git a/modules/bcftools/stats/meta.yml b/modules/bcftools/stats/meta.yml
index 304b88ec..b0aec1eb 100644
--- a/modules/bcftools/stats/meta.yml
+++ b/modules/bcftools/stats/meta.yml
@@ -19,6 +19,10 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
+  - target_bed:
+      type: file
+      description: target bed file
+      pattern: "*.{bed}"
   - vcf:
       type: file
       description: VCF input file
@@ -40,3 +44,4 @@ output:
 authors:
   - "@joseespinosa"
   - "@drpatelh"
+  - "@SusiJo"
diff --git a/tests/modules/bcftools/stats/main.nf b/tests/modules/bcftools/stats/main.nf
index 808a3330..b25cc6b2 100644
--- a/tests/modules/bcftools/stats/main.nf
+++ b/tests/modules/bcftools/stats/main.nf
@@ -6,8 +6,8 @@ include { BCFTOOLS_STATS } from '../../../../modules/bcftools/stats/main.nf'
 
 workflow test_bcftools_stats {
     input = [ [ id:'test' ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ],
             ]
 
-    BCFTOOLS_STATS ( input )
+    BCFTOOLS_STATS ( input, [] )
 }