From d596571a03161ee9992b0720c05084cb2ddef324 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 28 Jun 2022 16:18:12 +0200
Subject: [PATCH] added an optional vcf index to bcftools/norm (#1821)

* added an optional vcf index to bcftools/norm

* updated test.yml for failing conda tests
---
 modules/bcftools/norm/main.nf        |  2 +-
 modules/bcftools/norm/meta.yml       |  8 +++++++-
 tests/modules/bcftools/norm/main.nf  | 18 ++++++++++++++++--
 tests/modules/bcftools/norm/test.yml | 13 ++++++++++---
 4 files changed, 34 insertions(+), 7 deletions(-)

diff --git a/modules/bcftools/norm/main.nf b/modules/bcftools/norm/main.nf
index b81a4310..c48aa9bf 100644
--- a/modules/bcftools/norm/main.nf
+++ b/modules/bcftools/norm/main.nf
@@ -8,7 +8,7 @@ process BCFTOOLS_NORM {
         'quay.io/biocontainers/bcftools:1.14--h88f3f91_0' }"
 
     input:
-    tuple val(meta), path(vcf)
+    tuple val(meta), path(vcf), path(tbi)
     path(fasta)
 
     output:
diff --git a/modules/bcftools/norm/meta.yml b/modules/bcftools/norm/meta.yml
index ce4aee85..2b3c8eae 100644
--- a/modules/bcftools/norm/meta.yml
+++ b/modules/bcftools/norm/meta.yml
@@ -24,6 +24,12 @@ input:
       description: |
         The vcf file to be normalized
         e.g. 'file1.vcf'
+      pattern: "*.{vcf,vcf.gz}"
+  - tbi:
+      type: file
+      description: |
+        An optional index of the VCF file (for when the VCF is compressed)
+      pattern: "*.vcf.gz.tbi"
   - fasta:
       type: file
       description: FASTA reference file
@@ -37,7 +43,7 @@ output:
   - vcf:
       type: file
       description: VCF normalized output file
-      pattern: "*.{vcf.gz}"
+      pattern: "*.vcf.gz"
   - versions:
       type: file
       description: File containing software versions
diff --git a/tests/modules/bcftools/norm/main.nf b/tests/modules/bcftools/norm/main.nf
index ac056bea..a9ac75ba 100644
--- a/tests/modules/bcftools/norm/main.nf
+++ b/tests/modules/bcftools/norm/main.nf
@@ -4,10 +4,24 @@ nextflow.enable.dsl = 2
 
 include { BCFTOOLS_NORM } from '../../../../modules/bcftools/norm/main.nf'
 
-workflow test_bcftools_norm {
+workflow test_bcftools_norm_no_tbi {
     
     input = [ [ id:'test2', single_end:false ], // meta map
-              file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)]
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            []
+            ]
+
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+
+    BCFTOOLS_NORM ( input, fasta )
+}
+
+workflow test_bcftools_norm_tbi {
+    
+    input = [ [ id:'test2', single_end:false ], // meta map
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+            file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)            
+            ]
 
     fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
diff --git a/tests/modules/bcftools/norm/test.yml b/tests/modules/bcftools/norm/test.yml
index bb4f9aca..bdc3ce3f 100644
--- a/tests/modules/bcftools/norm/test.yml
+++ b/tests/modules/bcftools/norm/test.yml
@@ -1,8 +1,15 @@
-- name: bcftools norm
-  command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
+- name: bcftools norm test_bcftools_norm_no_tbi
+  command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_no_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
+  tags:
+    - bcftools
+    - bcftools/norm
+  files:
+    - path: output/bcftools/test2.vcf.gz
+
+- name: bcftools norm test_bcftools_norm_tbi
+  command: nextflow run ./tests/modules/bcftools/norm -entry test_bcftools_norm_tbi -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/norm/nextflow.config
   tags:
     - bcftools
     - bcftools/norm
   files:
     - path: output/bcftools/test2.vcf.gz
-      md5sum: 2b1cac07d1875b8adcd7a85346890f07