Kaiju2table module (#1545)

* Add kaiju2table module
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Sofia Stamouli 2022-04-22 11:26:30 +02:00 committed by GitHub
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process KAIJU_KAIJU2TABLE {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
'quay.io/biocontainers/kaiju:1.8.2--h2e03b76_0' }"
input:
tuple val(meta), path(results)
path db
val taxon_rank
output:
tuple val(meta), path('*.txt'), emit: summary
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}"
"""
dbnodes=`find -L ${db} -name "*nodes.dmp"`
dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
kaiju2table $args \\
-t \$dbnodes \\
-n \$dbname \\
-r ${taxon_rank} \\
-o ${prefix}.txt \\
${results}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
END_VERSIONS
"""
}

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name: "kaiju_kaiju2table"
description: write your description here
keywords:
- classify
- metagenomics
tools:
- kaiju:
description: Fast and sensitive taxonomic classification for metagenomics
homepage: https://kaiju.binf.ku.dk/
documentation: https://github.com/bioinformatics-centre/kaiju/blob/master/README.md
tool_dev_url: https://github.com/bioinformatics-centre/kaiju
doi: "10.1038/ncomms11257"
licence: ["GNU GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- results:
type: file
description: File containing the kaiju classification results
pattern: "*.{txt}"
- taxon_rank:
type: string
description: |
Taxonomic rank to display in report
pattern: "phylum|class|order|family|genus|species"
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"
- results:
type: file
description: |
Summary table for a given taxonomic rank
pattern: "*.{tsv}"
authors:
- "@sofstam"
- "@talnor"
- "@jfy133"

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@ -1009,6 +1009,10 @@ kaiju/kaiju:
- modules/kaiju/kaiju/** - modules/kaiju/kaiju/**
- tests/modules/kaiju/kaiju/** - tests/modules/kaiju/kaiju/**
kaiju/kaiju2table:
- modules/kaiju/kaiju2table/**
- tests/modules/kaiju/kaiju2table/**
kallisto/index: kallisto/index:
- modules/kallisto/index/** - modules/kallisto/index/**
- tests/modules/kallisto/index/** - tests/modules/kallisto/index/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { UNTAR } from '../../../../modules/untar/main.nf'
include { KAIJU_KAIJU } from '../../../../modules/kaiju/kaiju/main.nf'
include { KAIJU_KAIJU2TABLE } from '../../../../modules/kaiju/kaiju2table/main.nf'
workflow test_kaiju_kaiju_single_end {
input = [
[ id:'test', single_end:true ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
db = [ [], file(params.test_data['sarscov2']['genome']['kaiju_tar_gz'], checkIfExists: true) ]
taxon_rank = "species"
ch_db = UNTAR ( db )
KAIJU_KAIJU ( input, ch_db.untar.map{ it[1] } )
KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_db.untar.map{ it[1] }, taxon_rank )
}

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

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- name: kaiju kaiju2table test_kaiju_kaiju_single_end
command: nextflow run tests/modules/kaiju/kaiju2table -entry test_kaiju_kaiju_single_end -c tests/config/nextflow.config
tags:
- kaiju
- kaiju/kaiju2table
files:
- path: output/kaiju/test.txt
md5sum: 0d9f8fd36fcf2888296ae12632c5f0a8
- path: output/kaiju/versions.yml