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Add epang/place (#2023)
* Created epang module from template * Module seems to be working * Namechange to epang_place * Move model to meta map * Fix linting problems * Prettier * Forgot --threads! * Moved module to epang * Move reference file params * Directory output * Make all args optional * Added inputs for three other types of file arguments * Update modules/epang/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Add directory to output doc, reorder the other * Make model specification less hardcoded Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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56
modules/epang/main.nf
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56
modules/epang/main.nf
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process EPANG {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::epa-ng=0.3.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/epa-ng:0.3.8--h9a82719_1':
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'quay.io/biocontainers/epa-ng:0.3.8--h9a82719_1' }"
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input:
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tuple val(meta), path(queryaln)
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path referencealn
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path referencetree
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path bfastfile
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path splitfile
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path binaryfile
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output:
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tuple val(meta), path("./."), emit: epang , optional: true
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path "*.epa_result.jplace" , emit: jplace , optional: true
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path "*.epa_info.log" , emit: log
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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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def queryarg = queryaln ? "--query $queryaln" : ""
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def refalnarg = referencealn ? "--ref-msa $referencealn" : ""
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def reftreearg = referencetree ? "--tree $referencetree" : ""
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def bfastarg = bfastfile ? "--bfast $bfastfile" : ""
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def splitarg = splitfile ? "--split $splitfile" : ""
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def binaryarg = binaryfile ? "--binary $binaryfile" : ""
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if ( binaryfile && ( referencealn || referencetree ) ) error "[EPANG] Cannot supply both binary and reference MSA or reference tree. Check input"
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"""
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epa-ng \\
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$args \\
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--threads $task.cpus \\
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$queryarg \\
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$refalnarg \\
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$reftreearg \\
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$bfastarg \\
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$splitarg \\
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$binaryarg
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[ -e epa_result.jplace ] && mv epa_result.jplace ${prefix}.epa_result.jplace
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[ -e epa_info.log ] && mv epa_info.log ${prefix}.epa_info.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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epang: \$(echo \$(epa-ng --version 2>&1) | sed 's/^EPA-ng v//')
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END_VERSIONS
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"""
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}
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70
modules/epang/meta.yml
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70
modules/epang/meta.yml
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name: "epang"
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description: phylogenetic placement of query sequences in a reference tree
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keywords:
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- phylogeny
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- phylogenetic placement
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- sequences
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tools:
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- "epang":
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description: "Massively parallel phylogenetic placement of genetic sequences"
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homepage: "https://github.com/Pbdas/epa-ng"
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documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example"
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tool_dev_url: "https://github.com/Pbdas/epa-ng"
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doi: "https://doi.org/10.1093/sysbio/syy054"
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licence: "['GNU Affero General Public License v3.0']"
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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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e.g. [ id:'test' ]
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- queryaln:
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type: file
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description: aligned query sequences in any supported format including phylip and fasta, may be gzipped
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pattern: "*"
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- referencealn:
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type: file
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description: reference alignment in any supported format including phylip and fasta, may be gzipped
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pattern: "*"
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- referencetree:
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type: file
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description: newick file containing the reference tree in which query sequences will be placed
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pattern: "*"
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- bfastfile:
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type: file
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description: file argument to the --bfast parameter
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pattern: "*"
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- splitfile:
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type: file
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description: file argument to the --split parameter
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pattern: "*"
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- binaryfile:
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type: file
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description: file argument to the --binary parameter
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pattern: "*"
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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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e.g. [ id:'test' ]
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- epang:
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type: directory
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description: directory in which EPA-NG was run
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- jplace:
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type: file
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description: file with placement information
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pattern: "*.jplace"
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- log:
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type: file
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description: log file from placement
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pattern: "*.log"
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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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authors:
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- "@erikrikarddaniel"
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@ -719,6 +719,10 @@ entrezdirect/xtract:
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- modules/entrezdirect/xtract/**
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- modules/entrezdirect/xtract/**
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- tests/modules/entrezdirect/xtract/**
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- tests/modules/entrezdirect/xtract/**
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epang:
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- modules/epang/**
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- tests/modules/epang/
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expansionhunter:
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expansionhunter:
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- modules/expansionhunter/**
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- modules/expansionhunter/**
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- tests/modules/expansionhunter/**
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- tests/modules/expansionhunter/**
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22
tests/modules/epang/main.nf
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22
tests/modules/epang/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { EPANG } from '../../../modules/epang/main.nf'
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workflow test_epang {
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input = [
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[ id:'test', model:'LG' ], // meta map
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/query.alnfaa.gz', checkIfExists: true)
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]
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EPANG (
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input,
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.alnfaa.gz', checkIfExists: true),
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file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/epang/reference.newick', checkIfExists: true),
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[],
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[],
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[]
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)
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}
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7
tests/modules/epang/nextflow.config
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7
tests/modules/epang/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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ext.args = { " --model ${meta.model} " }
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}
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12
tests/modules/epang/test.yml
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12
tests/modules/epang/test.yml
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- name: epang test_epang
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command: nextflow run ./tests/modules/epang -entry test_epang -c ./tests/config/nextflow.config -c ./tests/modules/epang/nextflow.config
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tags:
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- epang
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files:
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- path: output/epang/test.epa_info.log
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contains:
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- "INFO 3 Sequences done"
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- path: output/epang/test.epa_result.jplace
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contains:
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- '"placements":'
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- '"metadata": {"invocation": "epa-ng --model LG --threads 2 --query query.alnfaa.gz --ref-msa reference.alnfaa.gz --tree reference.newick "}'
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