fix bgziptabix extension (#1784)

* fix bgziptabix extension * update test.yml
nf-core · Jun 15, 2022 · 9dbafff · 9dbafff
1 parent 0af6ade
commit 9dbafff
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diff --git 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
@@ -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