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Get fixed Krona module and add Krona taxonomy to test profile
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commit
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4 changed files with 12 additions and 7 deletions
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@ -38,6 +38,7 @@ params {
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run_centrifuge = true
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run_diamond = true
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run_krona = true
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krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
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malt_save_reads = true
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kraken2_save_reads = true
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centrifuge_save_reads = true
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@ -58,7 +58,7 @@
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"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
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},
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"krona/ktimporttaxonomy": {
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"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
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"git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
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},
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"krona/ktimporttext": {
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"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"
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@ -10,7 +10,7 @@ process KRONA_KTIMPORTTAXONOMY {
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input:
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tuple val(meta), path(report)
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path taxonomy
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path taxonomy, stageAs: 'taxonomy.tab'
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output:
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tuple val(meta), path ('*.html'), emit: html
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@ -24,10 +24,13 @@ process KRONA_KTIMPORTTAXONOMY {
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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
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echo \$TAXONOMY
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ktImportTaxonomy \\
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$args \\
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-o ${prefix}.html \\
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-tax $taxonomy \\
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-tax \$TAXONOMY/ \\
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$report
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cat <<-END_VERSIONS > versions.yml
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@ -35,4 +38,4 @@ process KRONA_KTIMPORTTAXONOMY {
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krona: $VERSION
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END_VERSIONS
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"""
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}
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}
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@ -25,9 +25,10 @@ input:
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- database:
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type: file
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description: |
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Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
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The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
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The parent folder will be passed as argument to ktImportTaxonomy.
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Path to a Krona taxonomy .tab file normally downloaded and generated by
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krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but
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must end in `.tab`.
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pattern: "*tab"
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- report:
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type: file
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description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored."
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