Merge pull request #1736 from genomic-medicine-sweden/rhocall

Add rhocall/annotate

modules/rhocall/annotate/main.nf

@@ -0,0 +1,51 @@
+process RHOCALL_ANNOTATE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::rhocall=0.5.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/rhocall:0.5.1--py39hbf8eff0_0':
+        'quay.io/biocontainers/rhocall:0.5.1--py39hbf8eff0_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta), path(roh)
+    path bed
+
+    output:
+    tuple val(meta), path("*_rhocall.vcf"), 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}"
+    def az_bed = bed ? "-b ${bed}" : ''
+    """
+    rhocall \\
+        annotate \\
+        $args \\
+        $az_bed \\
+        -r $roh \\
+        -o ${prefix}_rhocall.vcf \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_rhocall.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rhocall: \$(echo \$(rhocall --version 2>&1) | sed 's/rhocall, version //' )
+    END_VERSIONS
+    """
+}

modules/rhocall/annotate/meta.yml

@@ -0,0 +1,54 @@
+name: "rhocall_annotate"
+description: "Markup VCF file using rho-calls."
+keywords:
+  - roh
+  - rhocall
+tools:
+  - "rhocall":
+      description: "Call regions of homozygosity and make tentative UPD calls."
+      homepage: "https://github.com/dnil/rhocall"
+      documentation: "https://github.com/dnil/rhocall"
+      tool_dev_url: "https://github.com/dnil"
+      doi: ""
+      licence: "['GPL v3']"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: vcf file
+      pattern: "*.{vcf,vcf.gz}"
+  - tbi:
+      type: file
+      description: vcf index file
+      pattern: "*.{tbi}"
+  - roh:
+      type: file
+      description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL
+      pattern: "*.{roh}"
+  - bed:
+      type: file
+      description: BED file with AZ windows.
+      pattern: "*.{bed}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: vcf file
+      pattern: "*.{vcf,vcf.gz}"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ramprasadn"

tests/config/pytest_modules.yml

@@ -1647,6 +1647,10 @@ rgi/main:
   - modules/rgi/main/**
   - tests/modules/rgi/main/**
 
+rhocall/annotate:
+  - modules/rhocall/annotate/**
+  - tests/modules/rhocall/annotate/**
+
 rmarkdownnotebook:
   - modules/rmarkdownnotebook/**
   - tests/modules/rmarkdownnotebook/**

tests/modules/rhocall/annotate/main.nf

@@ -0,0 +1,40 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf'
+include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
+
+workflow test_rhocall_annotate {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
+
+}
+
+workflow test_rhocall_annotate_stub {
+
+    input = [ [ id:'test' ], // meta map
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
+             file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
+
+    af_file = [[],[]]
+    gen_map = []
+    regions = []
+    targets = []
+    samples = []
+
+    BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
+    RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
+
+}

tests/modules/rhocall/annotate/nextflow.config

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

tests/modules/rhocall/annotate/test.yml

@@ -0,0 +1,17 @@
+- name: "rhocall annotate"
+  command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config
+  tags:
+    - "rhocall"
+    - "rhocall/annotate"
+  files:
+    - path: "output/rhocall/test_rhocall.vcf"
+    - path: "output/rhocall/versions.yml"
+
+- name: "rhocall annotate stub"
+  command: nextflow run ./tests/modules/rhocall/annotate -entry test_rhocall_annotate_stub -c ./tests/config/nextflow.config -c ./tests/modules/rhocall/annotate/nextflow.config -stub-run
+  tags:
+    - "rhocall"
+    - "rhocall/annotate"
+  files:
+    - path: "output/rhocall/test_rhocall.vcf"
+    - path: "output/rhocall/versions.yml"