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>
This commit is contained in:
Mei Wu 2022-02-28 14:23:12 +01:00 committed by GitHub
parent 1ad73f1b2a
commit ef811d952b
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6 changed files with 119 additions and 0 deletions

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@ -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
"""
}

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@ -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"

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@ -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/**

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@ -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 )
}

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

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@ -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