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Update bracken so parameters come directly from database args
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parent
3dba6405c5
commit
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3 changed files with 7 additions and 7 deletions
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@ -23,7 +23,7 @@
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},
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"bracken/bracken": {
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"branch": "master",
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"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
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"git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
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},
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"cat/fastq": {
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"branch": "master",
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7
modules/nf-core/bracken/bracken/main.nf
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7
modules/nf-core/bracken/bracken/main.nf
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@ -21,12 +21,9 @@ process BRACKEN_BRACKEN {
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task.ext.when == null || task.ext.when
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script:
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def threshold = meta.threshold ?: 10
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def taxonomic_level = meta.taxonomic_level ?: 'S'
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def read_length = meta.read_length ?: 150
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def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
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def args = task.ext.args ?: ""
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def prefix = task.ext.prefix ?: "${meta.id}"
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bracken_report = "${prefix}_${taxonomic_level}.tsv"
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bracken_report = "${prefix}.tsv"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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5
modules/nf-core/bracken/bracken/meta.yml
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5
modules/nf-core/bracken/bracken/meta.yml
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@ -1,7 +1,10 @@
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name: bracken_bracken
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description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
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keywords:
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- sort
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- bracken
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- metagenomics
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- abundance
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- kraken2
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tools:
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- bracken:
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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.
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