Add stranger (#1360)

* Add stranger

* Add when clause

* Update paths

* Update modules/stranger/main.nf

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>

modules/stranger/main.nf

@@ -0,0 +1,33 @@
+process STRANGER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::stranger=0.8.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
+        'quay.io/biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
+
+    input:
+    tuple val(meta), path(vcf)
+
+    output:
+    tuple val(meta), path("*.gz"), emit: vcf
+    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}"
+    """
+    stranger \\
+        $args \\
+        $vcf | gzip --no-name > ${prefix}.vcf.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        stranger: \$( stranger --version )
+    END_VERSIONS
+    """
+}

modules/stranger/meta.yml

@@ -0,0 +1,44 @@
+name: stranger
+description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes.
+keywords:
+  - STR
+  - repeat_expansions
+  - annotate
+  - vcf
+tools:
+  - stranger:
+      description: Annotate VCF files with str variants
+      homepage: https://github.com/moonso/stranger
+      documentation: https://github.com/moonso/stranger
+      tool_dev_url: https://github.com/moonso/stranger
+      doi: "10.5281/zenodo.4548873"
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF with repeat expansions
+      pattern: "*.{vcf.gz,vcf}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - vcf:
+      type: file
+      description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin
+      pattern: "*.{vcf.gz}"
+
+authors:
+  - "@ljmesi"

tests/config/pytest_modules.yml

@@ -1565,6 +1565,10 @@ star/genomegenerate:
   - modules/star/genomegenerate/**
   - tests/modules/star/genomegenerate/**
 
+stranger:
+  - modules/stranger/**
+  - tests/modules/stranger/**
+
 strelka/germline:
   - modules/strelka/germline/**
   - tests/modules/strelka/germline/**

tests/modules/stranger/main.nf

@@ -0,0 +1,19 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
+include { STRANGER } from '../../../modules/stranger/main.nf'
+
+workflow test_stranger {
+
+    input = [ [ id:'test', gender:'male' ], // meta map
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
+            ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
+
+    EXPANSIONHUNTER ( input, fasta, variant_catalog )
+    STRANGER ( EXPANSIONHUNTER.out.vcf )
+}

tests/modules/stranger/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/modules/stranger/test.yml

@@ -0,0 +1,13 @@
+- name: stranger test_stranger
+  command: nextflow run tests/modules/stranger -entry test_stranger -c tests/config/nextflow.config
+  tags:
+    - stranger
+  files:
+    - path: output/expansionhunter/test.vcf
+      md5sum: cfd4a1d35c0e469b99eb6aaa6d22de76
+    - path: output/expansionhunter/versions.yml
+      md5sum: f3962a6eecfddf9682414c0f605a885a
+    - path: output/stranger/test.vcf.gz
+      md5sum: bbe15159195681d5c18596d3ad85c78f
+    - path: output/stranger/versions.yml
+      md5sum: 5ec35fd835fb1be50bc3e7c004310fc0