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Update KRAKENTOOLS/COMBINEKREPORTS (#2043)
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Add meta to combinekreports
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4 changed files with 17 additions and 7 deletions
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@ -7,10 +7,10 @@ process KRAKENTOOLS_COMBINEKREPORTS {
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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input:
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input:
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path kreports
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tuple val(meta), path(kreports)
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output:
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output:
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path "*.txt", emit: txt
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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path "versions.yml", emit: versions
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when:
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when:
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@ -18,12 +18,12 @@ process KRAKENTOOLS_COMBINEKREPORTS {
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "kreports_combined.txt"
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prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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"""
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combine_kreports.py \\
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combine_kreports.py \\
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-r ${kreports} \\
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-r ${kreports} \\
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-o ${prefix} \\
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-o ${prefix}.txt \\
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${args}
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${args}
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cat <<-END_VERSIONS > versions.yml
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cat <<-END_VERSIONS > versions.yml
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@ -14,12 +14,22 @@ tools:
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licence: ["GPL v3"]
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licence: ["GPL v3"]
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input:
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- kreports:
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- kreports:
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type: file
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type: file
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description: List of kraken-style report files
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description: List of kraken-style report files
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pattern: "*.{txt,kreport}"
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pattern: "*.{txt,kreport}"
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output:
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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- versions:
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type: file
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type: file
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description: File containing software versions
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description: File containing software versions
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@ -19,5 +19,5 @@ workflow test_krakentools_combinekreports {
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UNTAR ( db )
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UNTAR ( db )
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KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
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KRAKEN2_KRAKEN2 ( input, UNTAR.out.untar.map{ it[1] }, false, false )
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KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [ it[1] ] }.collect().dump() )
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KRAKENTOOLS_COMBINEKREPORTS ( KRAKEN2_KRAKEN2.out.report.map{ [[id:"test"], it[1]] }.groupTuple().dump())
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}
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}
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@ -1,9 +1,9 @@
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- name: krakentools combinekreports test_krakentools_combinekreports
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- name: krakentools combinekreports test_krakentools_combinekreports
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command: nextflow run ./tests/modules/krakentools/combinekreports -entry test_krakentools_combinekreports -c ./tests/config/nextflow.config -c ./tests/modules/krakentools/combinekreports/nextflow.config
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command: nextflow run ./tests/modules/krakentools/combinekreports -entry test_krakentools_combinekreports -c ./tests/config/nextflow.config -c ./tests/modules/krakentools/combinekreports/nextflow.config
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tags:
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tags:
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- krakentools/combinekreports
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- krakentools
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- krakentools
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- krakentools/combinekreports
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files:
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files:
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- path: output/krakentools/kreports_combined.txt
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- path: output/krakentools/test.txt
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contains:
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contains:
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- "#Number of Samples: 2"
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- "#Number of Samples: 2"
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