Merge branch 'master' into trigger_more_tests

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ repos:
         additional_dependencies:
           - [email protected]
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.2
+    rev: 0.29.3
     hooks:
       - id: check-jsonschema
         # match meta.ymls in one of the subdirectories of modules/nf-core

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

@@ -11,18 +11,22 @@ process BCFTOOLS_CONCAT {
     tuple val(meta), path(vcfs), path(tbi)
 
     output:
-    tuple val(meta), path("*.gz") , emit: vcf
-    tuple val(meta), path("*.tbi"), emit: tbi, optional: true
-    tuple val(meta), path("*.csi"), emit: csi, optional: true
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("${prefix}.vcf.gz")    , emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true
+    path  "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name }
+    def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n    ")
     """
+    ${create_input_index}
+
     bcftools concat \\
         --output ${prefix}.vcf.gz \\
         $args \\
@@ -37,7 +41,7 @@ process BCFTOOLS_CONCAT {
 
     stub:
     def args = task.ext.args   ?: ''
-    def prefix   = task.ext.prefix ?: "${meta.id}"
+    prefix   = task.ext.prefix ?: "${meta.id}"
     def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" :
                 args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" :
                 args.contains("--write-index") || args.contains("-W") ? "csi" :

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

@@ -37,29 +37,38 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.gz":
-          type: file
-          description: VCF concatenated output file
+          pattern: "*.{vcf.gz}"
+      - ${prefix}.vcf.gz:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.{vcf.gz}"
   - tbi:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.tbi":
-          type: file
-          description: Alternative VCF file index
+          pattern: "*.tbi"
+      - ${prefix}.vcf.gz.tbi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.tbi"
   - csi:
       - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "*.csi":
-          type: file
-          description: Default VCF file index
+          pattern: "*.csi"
+      - ${prefix}.vcf.gz.csi:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
           pattern: "*.csi"
   - versions:
       - versions.yml:

modules/nf-core/bcftools/concat/tests/main.nf.test

@@ -10,7 +10,7 @@ nextflow_process {
     tag "bcftools/concat"
 
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") {
 
         config "./nextflow.config"
 
@@ -41,7 +41,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") {
 
         config "./vcf_gz_index.config"
 
@@ -78,7 +78,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") {
 
         config "./vcf_gz_index_csi.config"
 
@@ -115,7 +115,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") {
 
         config "./vcf_gz_index_tbi.config"
 
@@ -153,7 +153,7 @@ nextflow_process {
     }
 
 
-    test("sarscov2 - [[vcf1, vcf2], []]") {
+    test("homo_sapiens - [[vcf1, vcf2], []]") {
 
         config "./nextflow.config"
 
@@ -181,7 +181,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") {
 
         config "./nextflow.config"
         options "-stub"
@@ -213,7 +213,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") {
 
         config "./vcf_gz_index.config"
         options "-stub"
@@ -246,7 +246,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") {
 
         config "./vcf_gz_index_csi.config"
         options "-stub"
@@ -279,7 +279,7 @@ nextflow_process {
 
     }
 
-    test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
+    test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") {
 
         config "./vcf_gz_index_tbi.config"
         options "-stub"