From 9dbaffff88013bc21460a989cde7a5aa172c2e0b Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Wed, 15 Jun 2022 10:33:10 +0200
Subject: [PATCH] fix bgziptabix extension (#1784)

* fix bgziptabix extension

* update test.yml
---
 modules/tabix/bgziptabix/main.nf        | 4 ++--
 tests/modules/tabix/bgziptabix/test.yml | 8 ++++----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf
index 77fd91a5..03e3b0c3 100644
--- a/modules/tabix/bgziptabix/main.nf
+++ b/modules/tabix/bgziptabix/main.nf
@@ -22,8 +22,8 @@ process TABIX_BGZIPTABIX {
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    bgzip  --threads ${task.cpus} -c $args $input > ${prefix}.gz
-    tabix $args2 ${prefix}.gz
+    bgzip  --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
+    tabix $args2 ${prefix}.${input.getExtension()}.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/tabix/bgziptabix/test.yml b/tests/modules/tabix/bgziptabix/test.yml
index 1bcfa88a..ed614d7e 100644
--- a/tests/modules/tabix/bgziptabix/test.yml
+++ b/tests/modules/tabix/bgziptabix/test.yml
@@ -1,10 +1,10 @@
-- name: tabix bgziptabix
+- name: tabix bgziptabix test_tabix_bgziptabix
   command: nextflow run ./tests/modules/tabix/bgziptabix -entry test_tabix_bgziptabix -c ./tests/config/nextflow.config -c ./tests/modules/tabix/bgziptabix/nextflow.config
   tags:
-    - tabix
     - tabix/bgziptabix
+    - tabix
   files:
-    - path: ./output/tabix/test.gz
+    - path: output/tabix/test.vcf.gz
       md5sum: fc178eb342a91dc0d1d568601ad8f8e2
-    - path: ./output/tabix/test.gz.tbi
+    - path: output/tabix/test.vcf.gz.tbi
       md5sum: 36e11bf96ed0af4a92caa91a68612d64