From 51b0a6e4f3b048a1eebeb86896fa0374771ca554 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 31 May 2022 15:15:58 +0200
Subject: [PATCH] Added optional input of index files to bcftools/concat

---
 modules/bcftools/concat/main.nf        |  2 +-
 modules/bcftools/concat/meta.yml       |  5 +++++
 tests/modules/bcftools/concat/main.nf  | 18 +++++++++++++++---
 tests/modules/bcftools/concat/test.yml | 15 ++++++++++++---
 4 files changed, 33 insertions(+), 7 deletions(-)

diff --git a/modules/bcftools/concat/main.nf b/modules/bcftools/concat/main.nf
index c0633ef7..257ee36f 100644
--- a/modules/bcftools/concat/main.nf
+++ b/modules/bcftools/concat/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_CONCAT {
         'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
-    tuple val(meta), path(vcfs)
+    tuple val(meta), path(vcfs), path(tbi)
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
diff --git a/modules/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml
index 3984276f..167dbe5a 100644
--- a/modules/bcftools/concat/meta.yml
+++ b/modules/bcftools/concat/meta.yml
@@ -25,6 +25,11 @@ input:
       description: |
         List containing 2 or more vcf files
         e.g. [ 'file1.vcf', 'file2.vcf' ]
+  - tbi:
+      type: files
+      description: |
+        List containing 2 or more index files (optional)
+        e.g. [ 'file1.tbi', 'file2.tbi' ]
 output:
   - meta:
       type: map
diff --git a/tests/modules/bcftools/concat/main.nf b/tests/modules/bcftools/concat/main.nf
index 8441d488..777dc5b8 100644
--- a/tests/modules/bcftools/concat/main.nf
+++ b/tests/modules/bcftools/concat/main.nf
@@ -4,13 +4,25 @@ nextflow.enable.dsl = 2
 
 include { BCFTOOLS_CONCAT } from '../../../../modules/bcftools/concat/main.nf'
 
-workflow test_bcftools_concat {
+workflow test_bcftools_concat_tbi {
     
     input = [ [ id:'test3' ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ]
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true) ]
+            ]
+
+    BCFTOOLS_CONCAT ( input )
+}
+
+workflow test_bcftools_concat_no_tbi {
+    
+    input = [ [ id:'test3' ], // meta map
+              [ file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+                file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) ],
+              []
             ]
 
-
     BCFTOOLS_CONCAT ( input )
 }
diff --git a/tests/modules/bcftools/concat/test.yml b/tests/modules/bcftools/concat/test.yml
index 7d04ebc6..0d12badc 100644
--- a/tests/modules/bcftools/concat/test.yml
+++ b/tests/modules/bcftools/concat/test.yml
@@ -1,8 +1,17 @@
-- name: bcftools concat test_bcftools_concat
-  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/concat/nextflow.config
+- name: bcftools concat test_bcftools_concat_tbi
+  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
   tags:
-    - bcftools/concat
     - bcftools
+    - bcftools/concat
+  files:
+    - path: output/bcftools/test3.vcf.gz
+      md5sum: 35c88bfaad20101062e98beb217d7137
+
+- name: bcftools concat test_bcftools_concat_no_tbi
+  command: nextflow run ./tests/modules/bcftools/concat -entry test_bcftools_concat_no_tbi -c ./tests/config/nextflow.config  -c ./tests/modules/bcftools/concat/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/concat
   files:
     - path: output/bcftools/test3.vcf.gz
       md5sum: 35c88bfaad20101062e98beb217d7137