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chore: install Bracken module

This commit is contained in:
Moritz E. Beber 2022-10-14 10:52:17 +02:00
parent 4e771ab2c7
commit 4352d35937
3 changed files with 94 additions and 0 deletions

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@ -21,6 +21,10 @@
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
},
"bracken/bracken": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
},
"cat/fastq": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"

45
modules/nf-core/bracken/bracken/main.nf generated Normal file
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process BRACKEN_BRACKEN {
tag "$meta.id"
label 'process_low'
// WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
input:
tuple val(meta), path(kraken_report)
path database
output:
tuple val(meta), path(bracken_report), emit: reports
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def threshold = meta.threshold ?: 10
def taxonomic_level = meta.taxonomic_level ?: 'S'
def read_length = meta.read_length ?: 150
def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
def prefix = task.ext.prefix ?: "${meta.id}"
bracken_report = "${prefix}_${taxonomic_level}.tsv"
// WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions.
def VERSION = '2.7'
"""
bracken \\
${args} \\
-d '${database}' \\
-i '${kraken_report}' \\
-o '${bracken_report}'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bracken: ${VERSION}
END_VERSIONS
"""
}

45
modules/nf-core/bracken/bracken/meta.yml generated Normal file
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name: bracken_bracken
description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
keywords:
- sort
tools:
- bracken:
description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.
homepage: https://ccb.jhu.edu/software/bracken/
documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual
tool_dev_url: https://github.com/jenniferlu717/Bracken
doi: "10.7717/peerj-cs.104"
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- kraken_report:
type: file
description: TSV file with six columns coming from kraken2 output
pattern: "*.{tsv}"
- database:
type: file
description: Directory containing the kraken2/Bracken files for analysis
pattern: "*"
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"
- reports:
type: file
description: TSV output report of the re-estimated abundances
pattern: "*.{tsv}"
authors:
- "@Midnighter"