mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:23:10 +00:00
chore: install Bracken module
This commit is contained in:
parent
4e771ab2c7
commit
4352d35937
3 changed files with 94 additions and 0 deletions
|
@ -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
45
modules/nf-core/bracken/bracken/main.nf
generated
Normal file
|
@ -0,0 +1,45 @@
|
|||
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
45
modules/nf-core/bracken/bracken/meta.yml
generated
Normal file
|
@ -0,0 +1,45 @@
|
|||
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"
|
Loading…
Reference in a new issue