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=3.5.0
+  - bioconda::paraphase=3.4.0
   # renovate: datasource=conda depName=bioconda/samtools
   - bioconda::samtools=1.23

modules/nf-core/paraphase/main.nf

@@ -4,9 +4,9 @@ process PARAPHASE {
 
     conda "${moduleDir}/environment.yml"
 
-    container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
-        ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/d2/d2f7e7ef6dd6def56bef5252c28a65f279d5fcef09a832510d0de1d6dab09194/data'
-        : 'community.wave.seqera.io/library/minimap2_paraphase_samtools:2c52f03fe994efa6'}"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7b/7bad1fc17553609844471ecfebff87f9797c0cf0c374c7c7662af23943edd365/data':
+        'community.wave.seqera.io/library/minimap2_paraphase_samtools:5cc32e174d09f608' }"
 
     input:
     tuple val(meta), path(bam), path(bai)
@@ -19,9 +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
-    tuple val("${task.process}"), val('minimap2'), eval("minimap2 --version"), topic: versions, emit: versions_minimap2
-    tuple val("${task.process}"), val('paraphase'), eval("paraphase --version"), topic: versions, emit: versions_paraphase
-    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
+    tuple val("${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
@@ -42,17 +42,26 @@ 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}":
+        minimap2: \$(minimap2 --version 2>&1)
+        paraphase: \$(paraphase --version)
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
     """
 
     stub:

modules/nf-core/paraphase/meta.yml

@@ -136,7 +136,7 @@ output:
       - samtools:
           type: string
           description: The name of the tool
-      - samtools version | sed '1!d;s/.* //':
+      - samtools --version | sed '1!d;s/.* //':
           type: eval
           description: The expression to obtain the version of the tool
 topics:
@@ -165,7 +165,7 @@ topics:
       - samtools:
           type: string
           description: The name of the tool
-      - samtools version | sed '1!d;s/.* //':
+      - samtools --version | sed '1!d;s/.* //':
           type: eval
           description: The expression to obtain the version of the tool
 authors:

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

@@ -93,7 +93,44 @@ nextflow_process {
                     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.findAll { key, val -> key.startsWith("versions")}
+                    process.out.findAll { key, val -> key.startsWith('versions') }
+                    ).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,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
                     ).match()
                 }
             )