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Update bracken so parameters come directly from database args

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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
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2
modules.json
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@ -23,7 +23,7 @@
}, },
"bracken/bracken": { "bracken/bracken": {
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
}, },
"cat/fastq": { "cat/fastq": {
"branch": "master", "branch": "master",

7
modules/nf-core/bracken/bracken/main.nf generated
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@ -21,12 +21,9 @@ process BRACKEN_BRACKEN {
task.ext.when == null || task.ext.when task.ext.when == null || task.ext.when
script: script:
def threshold = meta.threshold ?: 10 def args = task.ext.args ?: ""
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}" 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. // WARN: Version information not provided by tool on CLI.
// Please update version string below when bumping container versions. // Please update version string below when bumping container versions.
def VERSION = '2.7' def VERSION = '2.7'

5
modules/nf-core/bracken/bracken/meta.yml generated
View file

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