Merge pull request #1685 from genomic-medicine-sweden/rhocall

add bcftools/roh

modules/bcftools/roh/main.nf

@@ -0,0 +1,61 @@
+process BCFTOOLS_ROH {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.15.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15.1--h0ea216a_0':
+        'quay.io/biocontainers/bcftools:1.15.1--h0ea216a_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    path af_file
+    path genetic_map
+    path regions_file
+    path samples_file
+    path targets_file
+
+    output:
+    tuple val(meta), path("*.roh"), emit: roh
+    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 af_read   = af_file         ? "--AF-file ${af_file}"           : ''
+    def gen_map   = genetic_map     ? "--genetic-map ${genetic_map}"   : ''
+    def reg_file  = regions_file    ? "--regions-file ${regions_file}" : ''
+    def samp_file = samples_file    ? "--samples-file ${samples_file}" : ''
+    def targ_file = targets_file    ? "--targets-file ${targets_file}" : ''
+    """
+    bcftools \\
+        roh \\
+        $args \\
+        $af_read \\
+        $gen_map \\
+        $reg_file \\
+        $samp_file \\
+        $targ_file \\
+        -o ${prefix}.roh \\
+        $vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix    = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.roh
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/bcftools/roh/meta.yml

@@ -0,0 +1,55 @@
+name: "bcftools_roh"
+description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
+keywords:
+  - roh
+tools:
+  - "roh":
+      description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered."
+      homepage: https://www.htslib.org/
+      documentation: http://www.htslib.org/doc/bcftools.html
+      doi: 10.1093/bioinformatics/btp352
+      licence: ["MIT"]
+
+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}"
+  - af_file:
+      type: file
+      description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
+  - genetic_map:
+      type: file
+      description: "Genetic map in the format required also by IMPUTE2."
+  - regions_file:
+      type: file
+      description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
+  - samples_file:
+      type: file
+      description: "File of sample names to include or exclude if prefixed with '^'."
+  - targets_file:
+      type: file
+      description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
+
+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"
+  - roh:
+      type: file
+      description: Contains site-specific and/or per-region runs of homo/autozygosity calls.
+      pattern: "*.{roh}"
+
+authors:
+  - "@ramprasadn"

tests/config/pytest_modules.yml

@@ -166,6 +166,10 @@ bcftools/reheader:
   - modules/bcftools/reheader/**
   - tests/modules/bcftools/reheader/**
 
+bcftools/roh:
+  - modules/bcftools/roh/**
+  - tests/modules/bcftools/roh/**
+
 bcftools/sort:
   - modules/bcftools/sort/**
   - tests/modules/bcftools/sort/**

tests/modules/bcftools/roh/main.nf

@@ -0,0 +1,35 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
+
+workflow test_bcftools_roh {
+
+    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 )
+}
+
+workflow test_bcftools_roh_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 )
+}

tests/modules/bcftools/roh/nextflow.config

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

tests/modules/bcftools/roh/test.yml

@@ -0,0 +1,17 @@
+- name: "bcftools roh"
+  command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
+  tags:
+    - "bcftools"
+    - "bcftools/roh"
+  files:
+    - path: "output/bcftools/test.roh"
+    - path: "output/bcftools/versions.yml"
+
+- name: "bcftools roh stub"
+  command: nextflow run ./tests/modules/bcftools/roh -entry test_bcftools_roh_stub -c ./tests/config/nextflow.config -c ./tests/modules/bcftools/roh/nextflow.config
+  tags:
+    - "bcftools"
+    - "bcftools/roh"
+  files:
+    - path: "output/bcftools/test.roh"
+    - path: "output/bcftools/versions.yml"