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Update bracken so parameters come directly from database args

This commit is contained in:
James Fellows Yates 2022-12-07 07:27:40 +01:00
parent 3dba6405c5
commit d8751787ac
3 changed files with 7 additions and 7 deletions

View file

@ -23,7 +23,7 @@
},
"bracken/bracken": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
},
"cat/fastq": {
"branch": "master",

View file

@ -21,12 +21,9 @@ process BRACKEN_BRACKEN {
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 ${read_length}"
def args = task.ext.args ?: ""
def prefix = task.ext.prefix ?: "${meta.id}"
bracken_report = "${prefix}_${taxonomic_level}.tsv"
bracken_report = "${prefix}.tsv"
// WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions.
def VERSION = '2.7'

View file

@ -1,7 +1,10 @@
name: bracken_bracken
description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
keywords:
- sort
- bracken
- metagenomics
- abundance
- kraken2
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.