diff --git a/modules.json b/modules.json index f2b6da8..fb721a8 100644 --- a/modules.json +++ b/modules.json @@ -23,7 +23,7 @@ }, "bracken/bracken": { "branch": "master", - "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" + "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1" }, "cat/fastq": { "branch": "master", diff --git a/modules/nf-core/bracken/bracken/main.nf b/modules/nf-core/bracken/bracken/main.nf index 5e08418..ac7d1af 100644 --- a/modules/nf-core/bracken/bracken/main.nf +++ b/modules/nf-core/bracken/bracken/main.nf @@ -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' diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml index 1931161..4a05edd 100644 --- a/modules/nf-core/bracken/bracken/meta.yml +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -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.