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Install KRAKENTOOLS_KREPORT2KRONA module

This commit is contained in:
Thomas A. Christensen II 2022-06-14 08:13:36 -05:00
parent 3dcda7446b
commit a84f693479
Signed by: millironx
GPG key ID: 139C07724802BC5D
3 changed files with 80 additions and 0 deletions

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@ -48,6 +48,9 @@
"kraken2/kraken2": {
"git_sha": "abe025677cdd805cc93032341ab19885473c1a07"
},
"krakentools/kreport2krona": {
"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
},
"malt/run": {
"git_sha": "72b96f4e504eef673f2b5c13560a9d90b669129b"
},

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def VERSION = '1.2' // Version information not provided by tool on CLI
process KRAKENTOOLS_KREPORT2KRONA {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
input:
tuple val(meta), path(kreport)
output:
tuple val(meta), path("*.txt"), emit: txt
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
"""
kreport2krona.py \\
-r ${kreport} \\
-o ${prefix}.txt \\
${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kreport2krona.py: ${VERSION}
END_VERSIONS
"""
}

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name: krakentools_kreport2krona
description: Takes a Kraken report file and prints out a krona-compatible TEXT file
keywords:
- kraken
- krona
- metagenomics
- visualization
tools:
- krakentools:
description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
homepage: https://github.com/jenniferlu717/KrakenTools
licence: ["GPL v3"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- kreport:
type: file
description: Kraken report
pattern: "*.{txt,kreport}"
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"
- krona:
type: file
description: Krona text-based input file converted from Kraken report
pattern: "*.{txt,krona}"
authors:
- "@MillironX"