Paraphase update

modules/nf-core/paraphase/environment.yml

@@ -8,6 +8,6 @@ dependencies:
   # renovate: datasource=conda depName=bioconda/minimap2
   - bioconda::minimap2=2.30
   # renovate: datasource=conda depName=bioconda/paraphase
-  - bioconda::paraphase=3.3.4
+  - bioconda::paraphase=3.4.0
   # renovate: datasource=conda depName=bioconda/samtools
-  - bioconda::samtools=1.22.1
+  - bioconda::samtools=1.23

modules/nf-core/paraphase/main.nf

@@ -6,7 +6,7 @@ process PARAPHASE {
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/65e79cfe3a98637330bad85befbbb0baf72366040ce1911f60be8485eae28d55/data':
-        'community.wave.seqera.io/library/minimap2_paraphase_samtools:ab39f9ad1f898e08' }"
+        'community.wave.seqera.io/library/minimap2_paraphase_samtools:5cc32e174d09f608' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -19,7 +19,9 @@ process PARAPHASE {
     tuple val(meta), path("*.paraphase.bam.bai")                        , emit: bai
     tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz")          , emit: vcf      , optional: true
     tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true
-    path "versions.yml"                                                 , emit: versions
+    tuple val("${task.process}"), val('minimap2'),  eval('minimap2 --version')      , emit: versions_minimap2   , topic: versions
+    tuple val("${task.process}"), val('paraphase'), eval('paraphase --version')     , emit: versions_paraphase  , topic: versions
+    tuple val("${task.process}"), val('samtools'),  eval('samtools --version | sed \'1!d;s/.* //\'')    , emit: versions_samtools   , topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -40,17 +42,19 @@ process PARAPHASE {
         $config_file \\
         --out .
 
-    for vcf in ${prefix}_paraphase_vcfs/*.vcf;
-    do
-        bgzip \\
-            $args2 \\
-            --threads $task.cpus \\
-            \$vcf;
-        tabix \\
-            $args3 \\
-            --threads $task.cpus \\
-            \$vcf.gz;
-    done
+    if compgen -G "${prefix}_paraphase_vcfs/*.vcf" > /dev/null; then
+        for vcf in ${prefix}_paraphase_vcfs/*.vcf;
+        do
+            bgzip \\
+                $args2 \\
+                --threads $task.cpus \\
+                \$vcf;
+            tabix \\
+                $args3 \\
+                --threads $task.cpus \\
+                \$vcf.gz;
+        done
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/paraphase/meta.yml

@@ -1,4 +1,3 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "paraphase"
 description: "HiFi-based caller for highly homologous genes"
 keywords:
@@ -12,9 +11,9 @@ tools:
       documentation: "https://github.com/PacificBiosciences/paraphase"
       tool_dev_url: "https://github.com/PacificBiosciences/paraphase"
       doi: "10.1016/j.ajhg.2023.01.001"
-      licence: ["BSD-3-clause-Clear"]
+      licence:
+        - "BSD-3-clause-Clear"
       identifier: ""
-
 input:
   - - meta:
         type: map
@@ -51,7 +50,7 @@ input:
         description: Config file
         pattern: "*.yaml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
 output:
   json:
     - - meta:
@@ -64,7 +63,7 @@ output:
           description: Summary of haplotype and variant calls
           pattern: "*.paraphase.json"
           ontologies:
-            - edam: http://edamontology.org/format_3464 # JSON
+            - edam: http://edamontology.org/format_3464
   bam:
     - - meta:
           type: map
@@ -98,7 +97,7 @@ output:
           description: compressed VCF file(s) per gene
           pattern: "*.vcf.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   vcf_index:
     - - meta:
           type: map
@@ -110,13 +109,65 @@ output:
           description: compressed VCF file index
           pattern: "*.vcf.gz.{tbi,csi}"
           ontologies: []
+  versions_minimap2:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - minimap2:
+          type: string
+          description: The name of the tool
+      - minimap2 --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_paraphase:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - paraphase:
+          type: string
+          description: The name of the tool
+      - paraphase --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - minimap2:
+          type: string
+          description: The name of the tool
+      - minimap2 --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - paraphase:
+          type: string
+          description: The name of the tool
+      - paraphase --version:
+          type: eval
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools --version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@fellen31"
 maintainers:

modules/nf-core/paraphase/tests/main.nf.test

@@ -53,8 +53,7 @@ nextflow_process {
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     bam(process.out.bam.get(0).get(1)).getReadsMD5(),
                     file(process.out.bai.get(0).get(1)).name,
-                    file(process.out.vcf_index.get(0).get(1)).name,
-                    process.out.versions
+                    file(process.out.vcf_index.get(0).get(1)).name
                     ).match()
                 }
             )
@@ -92,8 +91,43 @@ nextflow_process {
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     bam(process.out.bam.get(0).get(1)).getReadsMD5(),
                     file(process.out.bai.get(0).get(1)).name,
-                    file(process.out.vcf_index.get(0).get(1)).name,
-                    process.out.versions
+                    file(process.out.vcf_index.get(0).get(1)).name
+                    ).match()
+                }
+            )
+        }
+    }
+
+    test("homo_sapiens - [ bam, bai ], no_vcf") {
+
+        config "./nextflow.no_vcf.config"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true),
+                ]
+                input[1] = TABIX_BGZIP.out.output
+                input[2] = [
+                    [ id:'test_config' ],
+                    file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.vcf?.isEmpty() },
+                { assert process.out.vcf_index?.isEmpty() },
+                { assert snapshot(
+                    file(process.out.json.get(0).get(1)),
+                    process.out.bam.get(0).get(1).isEmpty(),
+                    file(process.out.bai.get(0).get(1)).name
                     ).match()
                 }
             )
@@ -130,8 +164,7 @@ nextflow_process {
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
                     bam(process.out.bam.get(0).get(1)).getReadsMD5(),
                     file(process.out.bai.get(0).get(1)).name,
-                    file(process.out.vcf_index.get(0).get(1)).name,
-                    process.out.versions
+                    file(process.out.vcf_index.get(0).get(1)).name
                     ).match()
                 }
             )