From 8214b737004879e5c84081f8fcd00bb2203c68cb Mon Sep 17 00:00:00 2001
From: WackerO <43847497+WackerO@users.noreply.github.com>
Date: Wed, 20 Jul 2022 10:54:06 +0200
Subject: [PATCH] SVDB_MERGE bgzip (#1910)

* Started (again) to work on bgzipping SVDB_MERGE output

* Updated test yml

* SVDB_MERGE now bgzips output

* Fixed singularity, renamed tests in test.yml

Co-authored-by: Cloud User <centos@oskar-instance.novalocal>
---
 modules/svdb/merge/main.nf        | 10 +++++-----
 modules/svdb/merge/meta.yml       |  2 +-
 tests/modules/svdb/merge/test.yml |  8 ++++----
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/svdb/merge/main.nf b/modules/svdb/merge/main.nf
index 0d56fea2..365718af 100644
--- a/modules/svdb/merge/main.nf
+++ b/modules/svdb/merge/main.nf
@@ -1,18 +1,17 @@
 process SVDB_MERGE {
     tag "$meta.id"
     label 'process_medium'
-
-    conda (params.enable_conda ? "bioconda::svdb=2.6.1" : null)
+    conda (params.enable_conda ? "bioconda::svdb=2.6.1 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/svdb:2.6.1--py39h5371cbf_0':
-        'quay.io/biocontainers/svdb:2.6.1--py39h5371cbf_0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0':
+        'quay.io/biocontainers/mulled-v2-c8daa8f9d69d3c5a1a4ff08283a166c18edb0000:56d0a468970fbb474d92f0591abcf677757fb370-0' }"
 
     input:
     tuple val(meta), path(vcfs)
     val (priority)
 
     output:
-    tuple val(meta), path("*_sv_merge.vcf"), emit: vcf
+    tuple val(meta), path("*_sv_merge.vcf.gz"), emit: vcf
     path "versions.yml"           , emit: versions
 
     when:
@@ -37,6 +36,7 @@ process SVDB_MERGE {
         $prio \\
         --vcf $input \\
         > ${prefix}_sv_merge.vcf
+    bgzip ${prefix}_sv_merge.vcf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/svdb/merge/meta.yml b/modules/svdb/merge/meta.yml
index e166bad0..c71279e8 100644
--- a/modules/svdb/merge/meta.yml
+++ b/modules/svdb/merge/meta.yml
@@ -34,6 +34,6 @@ output:
   - vcf:
       type: file
       description: merged VCF file
-      pattern: "*_sv_merge.vcf"
+      pattern: "*_sv_merge.vcf.gz"
 authors:
   - "@ramprasadn"
diff --git a/tests/modules/svdb/merge/test.yml b/tests/modules/svdb/merge/test.yml
index 46c4fef0..12355020 100644
--- a/tests/modules/svdb/merge/test.yml
+++ b/tests/modules/svdb/merge/test.yml
@@ -1,14 +1,14 @@
-- name: svdb merge
+- name: svdb merge test_svdb_merge
   command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
   tags:
     - svdb
     - svdb/merge
   files:
-    - path: output/svdb/test_sv_merge.vcf
-- name: svdb merge noprio
+    - path: output/svdb/test_sv_merge.vcf.gz
+- name: svdb merge test_svdb_merge_noprio
   command: nextflow run ./tests/modules/svdb/merge -entry test_svdb_merge_noprio -c ./tests/config/nextflow.config -c ./tests/modules/svdb/merge/nextflow.config
   tags:
     - svdb
     - svdb/merge
   files:
-    - path: output/svdb/test_sv_merge.vcf
+    - path: output/svdb/test_sv_merge.vcf.gz