bcftools/annotate ready2go (#1291)

* bcf annotate ready2go

* edited output name

* fixed output

* updated bcftools ver

* changed contain output string

* removed contain key entirely

* fixed md5sum for test.yml

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>

modules/bcftools/annotate/main.nf

@@ -0,0 +1,42 @@
+process BCFTOOLS_ANNOTATE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::bcftools=1.15" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/bcftools:1.15--haf5b3da_0':
+        'quay.io/biocontainers/bcftools:1.15--haf5b3da_0' }"
+
+    input:
+    tuple val(meta), path(input)
+
+    output:
+    tuple val(meta), path("*_annotated.vcf.gz"), optional:true , emit: vcf
+    tuple val(meta), path("*_annotated.bcf")   , optional:true , emit: bcf
+    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 matcher = input =~ /vcf/
+    def output_suffix = matcher ? "vcf.gz" : "bcf"
+    def output_type_compressed = matcher ? "z" : "b"
+    """
+    bcftools \\
+        annotate \\
+        $args \\
+        --output ${prefix}_annotated.${output_suffix} \\
+        --output-type $output_type_compressed \\
+        --threads $task.cpus \\
+        $input
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
+    """
+}

modules/bcftools/annotate/meta.yml

@@ -0,0 +1,45 @@
+name: bcftools_annotate
+description: Add or remove annotations.
+keywords:
+  - bcftools
+  - annotate
+  - vcf
+  - remove
+  - add
+tools:
+  - annotate:
+      description: Add or remove annotations.
+      homepage: http://samtools.github.io/bcftools/bcftools.html
+      documentation: https://samtools.github.io/bcftools/bcftools.html#annotate
+      doi: 10.1093/bioinformatics/btp352
+      licence: ['MIT']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - input:
+      type: files
+      description: Query VCF or BCF file, can be either uncompressed or compressed
+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: Compressed annotated VCF file
+      pattern: "*_annotated.vcf.gz"
+  - bcf:
+      type: file
+      description: Compressed annotated BCF file
+      pattern: "*_annotated.bcf"
+authors:
+  - "@projectoriented"

tests/config/pytest_modules.yml

@@ -98,6 +98,10 @@ bbmap/index:
   - modules/bbmap/index/**
   - tests/modules/bbmap/index/**
 
+bcftools/annotate:
+  - modules/bcftools/annotate/**
+  - tests/modules/bcftools/annotate/**
+
 bcftools/concat:
   - modules/bcftools/concat/**
   - tests/modules/bcftools/concat/**

tests/modules/bcftools/annotate/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BCFTOOLS_ANNOTATE } from '../../../../modules/bcftools/annotate/main.nf'
+
+workflow test_bcftools_annotate {
+    
+    input = [ 
+    [ id:'test_compressed', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true) ]
+
+    BCFTOOLS_ANNOTATE ( input )
+}

tests/modules/bcftools/annotate/nextflow.config

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

tests/modules/bcftools/annotate/test.yml

@@ -0,0 +1,9 @@
+- name: bcftools annotate test_bcftools_annotate
+  command: nextflow run tests/modules/bcftools/annotate -entry test_bcftools_annotate -c tests/config/nextflow.config
+  tags:
+    - bcftools/annotate
+    - bcftools
+  files:
+    - path: output/bcftools/test_compressed_annotated.vcf.gz
+    - path: output/bcftools/versions.yml
+      md5sum: b647b465acc221f6fe6fbcc319724eed