From 13631304102ca3d99def3578611b79332f6fd175 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Fri, 24 Jun 2022 08:58:26 +0200
Subject: [PATCH] small changes to vcfanno (#1804)

removed a redundant input field from vcfanno

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/vcfanno/main.nf        |  4 +---
 tests/modules/vcfanno/main.nf  | 15 +++++----------
 tests/modules/vcfanno/test.yml | 20 ++++++++++----------
 3 files changed, 16 insertions(+), 23 deletions(-)

diff --git a/modules/vcfanno/main.nf b/modules/vcfanno/main.nf
index bc0514c9..6f264af2 100644
--- a/modules/vcfanno/main.nf
+++ b/modules/vcfanno/main.nf
@@ -9,7 +9,6 @@ process VCFANNO {
 
     input:
     tuple val(meta), path(vcf), path(tbi)
-    tuple val(meta), path(vcf_uncompressed)
     path toml
     path resource_dir
 
@@ -23,7 +22,6 @@ process VCFANNO {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def input_vcf = vcf_uncompressed ?: vcf
     """
     ln -sf $resource_dir/* \$(pwd)
 
@@ -31,7 +29,7 @@ process VCFANNO {
         -p $task.cpus \\
         $args \\
         $toml \\
-        $input_vcf \\
+        $vcf \\
         > ${prefix}_annotated.vcf
 
     cat <<-END_VERSIONS > versions.yml
diff --git a/tests/modules/vcfanno/main.nf b/tests/modules/vcfanno/main.nf
index c879ebbd..a1fe7c1a 100644
--- a/tests/modules/vcfanno/main.nf
+++ b/tests/modules/vcfanno/main.nf
@@ -13,29 +13,24 @@ workflow test_vcfanno {
         file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)
     ]
 
-    input_2 = [ [ id:'test_compressed', single_end:false ], // meta map
-                [] ]
-
     toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
     resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( resource_dir )
-    VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
+    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
 }
 
 workflow test_vcfanno_uncompressed {
 
-    input = [ [ id:'test_uncompressed', single_end:false ], // meta map
-                [] ,[] ]
-
-    input_2 = [
+    input = [ 
         [ id:'test_uncompressed', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+        [] 
     ]
 
     toml = file(params.test_data['homo_sapiens']['genome']['vcfanno_toml'], checkIfExists: true)
     resource_dir = [[], file(params.test_data['homo_sapiens']['genome']['vcfanno_tar_gz'], checkIfExists: true) ]
 
     UNTAR ( resource_dir )
-    VCFANNO ( input, input_2, toml, UNTAR.out.untar.map{ it[1] } )
+    VCFANNO ( input, toml, UNTAR.out.untar.map{ it[1] } )
 }
diff --git a/tests/modules/vcfanno/test.yml b/tests/modules/vcfanno/test.yml
index eae5d3b0..cb9a8b04 100644
--- a/tests/modules/vcfanno/test.yml
+++ b/tests/modules/vcfanno/test.yml
@@ -1,23 +1,23 @@
 - name: vcfanno test_vcfanno
-  command: nextflow run tests/modules/vcfanno -entry test_vcfanno -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno -c ./tests/config/nextflow.config  -c ./tests/modules/vcfanno/nextflow.config
   tags:
     - vcfanno
   files:
-    - path: output/untar/versions.yml
-      md5sum: 6de038155bccbe4d264d09529bf9f4d8
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
+      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
+      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
     - path: output/vcfanno/test_compressed_annotated.vcf
       md5sum: 90ceb2fd2e06e781846d69c3981db665
-    - path: output/vcfanno/versions.yml
-      md5sum: 62d13540503b22f04a2280c91942cb03
 
 - name: vcfanno test_vcfanno_uncompressed
-  command: nextflow run tests/modules/vcfanno -entry test_vcfanno_uncompressed -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/vcfanno -entry test_vcfanno_uncompressed -c ./tests/config/nextflow.config  -c ./tests/modules/vcfanno/nextflow.config
   tags:
     - vcfanno
   files:
-    - path: output/untar/versions.yml
-      md5sum: a0de70274caac0cca31b077a1e7172d9
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz
+      md5sum: eba4b55d81148d9c316cda68a5c0ad6d
+    - path: output/untar/vcfanno_grch38_module_test/exac.vcf.gz.tbi
+      md5sum: ec47aa09f0248f4f32ae12fb7ba03f34
     - path: output/vcfanno/test_uncompressed_annotated.vcf
       md5sum: 90ceb2fd2e06e781846d69c3981db665
-    - path: output/vcfanno/versions.yml
-      md5sum: 300218dad68c3ffcc4783daa4f7c5a43