Update bcftools view script (nf-core#4850)

* update test

* vcf output

* update snap

modules/nf-core/bcftools/view/main.nf

@@ -14,8 +14,8 @@ process BCFTOOLS_VIEW {
     path(samples)
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
+    path "versions.yml"                               , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,9 +26,14 @@ process BCFTOOLS_VIEW {
     def regions_file  = regions ? "--regions-file ${regions}" : ""
     def targets_file = targets ? "--targets-file ${targets}" : ""
     def samples_file =  samples ? "--samples-file ${samples}" : ""
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
     """
     bcftools view \\
-        --output ${prefix}.vcf.gz \\
+        --output ${prefix}.${extension} \\
         ${regions_file} \\
         ${targets_file} \\
         ${samples_file} \\
@@ -44,8 +49,13 @@ process BCFTOOLS_VIEW {
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" :
+                    args.contains("--output-type u") || args.contains("-Ou") ? "bcf" :
+                    args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" :
+                    args.contains("--output-type v") || args.contains("-Ov") ? "vcf" :
+                    "vcf"
     """
-    touch ${prefix}.vcf.gz
+    touch ${prefix}.${extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/bcftools/view/meta.yml

@@ -53,7 +53,7 @@ output:
   - vcf:
       type: file
       description: VCF normalized output file
-      pattern: "*.{vcf.gz}"
+      pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
   - versions:
       type: file
       description: File containing software versions

modules/nf-core/bcftools/view/tests/nextflow.config

@@ -1,3 +1,3 @@
 process {
-    ext.args = '--no-version'
-}
+    ext.args = '--no-version --output-type v'
+}