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Merge branch 'master' into biobambam/bammerge
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45
modules/hmtnote/main.nf
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45
modules/hmtnote/main.nf
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process HMTNOTE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
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'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_0' }"
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input:
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tuple val(meta), path(vcf)
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output:
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tuple val(meta), path("*_annotated.vcf"), emit: vcf
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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hmtnote \\
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annotate \\
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$vcf \\
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${prefix}_annotated.vcf \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_annotated.vcf
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
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END_VERSIONS
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"""
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}
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39
modules/hmtnote/meta.yml
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39
modules/hmtnote/meta.yml
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name: hmtnote
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description: Human mitochondrial variants annotation using HmtVar.
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keywords:
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- hmtnote mitochondria annotation
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tools:
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- hmtnote:
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description: Human mitochondrial variants annotation using HmtVar.
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homepage: https://github.com/robertopreste/HmtNote
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documentation: https://hmtnote.readthedocs.io/en/latest/usage.html
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tool_dev_url: None
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doi: "https://doi.org/10.1101/600619"
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licence: ["MIT"]
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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- vcf:
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type: file
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description: vcf file
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pattern: "*.vcf"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- vcf:
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type: file
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description: annotated vcf
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pattern: "*_annotated.vcf"
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authors:
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- "@sysbiocoder"
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@ -970,6 +970,10 @@ hmmer/hmmsearch:
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- modules/hmmer/hmmsearch/**
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- tests/modules/hmmer/hmmsearch/**
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hmtnote:
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- modules/hmtnote/**
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- tests/modules/hmtnote/**
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homer/annotatepeaks:
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- modules/homer/annotatepeaks/**
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- tests/modules/homer/annotatepeaks/**
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14
tests/modules/hmtnote/main.nf
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14
tests/modules/hmtnote/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { HMTNOTE } from '../../../modules/hmtnote/main.nf'
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workflow test_hmtnote {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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]
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HMTNOTE ( input)
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}
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7
tests/modules/hmtnote/nextflow.config
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7
tests/modules/hmtnote/nextflow.config
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: HMTNOTE {
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ext.args = '--basic --variab'
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}
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}
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6
tests/modules/hmtnote/test.yml
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6
tests/modules/hmtnote/test.yml
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- name: hmtnote test_hmtnote
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command: nextflow run ./tests/modules/hmtnote -entry test_hmtnote -c ./tests/config/nextflow.config -c ./tests/modules/hmtnote/nextflow.config
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tags:
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- hmtnote
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files:
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- path: output/hmtnote/test_annotated.vcf
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