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Get fixed Krona module and add Krona taxonomy to test profile

This commit is contained in:
James Fellows Yates 2022-07-01 17:21:19 +02:00
parent 97e6cdf4b4
commit 447b8f0905
4 changed files with 12 additions and 7 deletions

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@ -38,6 +38,7 @@ params {
run_centrifuge = true
run_diamond = true
run_krona = true
krona_taxonomy_directory = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab'
malt_save_reads = true
kraken2_save_reads = true
centrifuge_save_reads = true

View file

@ -58,7 +58,7 @@
"git_sha": "8b2a473f586bed003e72d2b183acc43fc0ddc422"
},
"krona/ktimporttaxonomy": {
"git_sha": "233fa70811a03a4cecb2ece483b5c8396e2cee1d"
"git_sha": "0e9fd9370ad1845870b8a9c63fcc47d999a1739e"
},
"krona/ktimporttext": {
"git_sha": "cdefbec66999c0b49d8bfeea9d6f9d19056635a2"

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@ -10,7 +10,7 @@ process KRONA_KTIMPORTTAXONOMY {
input:
tuple val(meta), path(report)
path taxonomy
path taxonomy, stageAs: 'taxonomy.tab'
output:
tuple val(meta), path ('*.html'), emit: html
@ -24,10 +24,13 @@ process KRONA_KTIMPORTTAXONOMY {
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
echo \$TAXONOMY
ktImportTaxonomy \\
$args \\
-o ${prefix}.html \\
-tax $taxonomy \\
-tax \$TAXONOMY/ \\
$report
cat <<-END_VERSIONS > versions.yml
@ -35,4 +38,4 @@ process KRONA_KTIMPORTTAXONOMY {
krona: $VERSION
END_VERSIONS
"""
}
}

View file

@ -25,9 +25,10 @@ input:
- database:
type: file
description: |
Path to the taxonomy database .tab file downloaded by krona/ktUpdateTaxonomy
The file will be saved under a folder named "taxonomy" as "taxonomy/taxonomy.tab".
The parent folder will be passed as argument to ktImportTaxonomy.
Path to a Krona taxonomy .tab file normally downloaded and generated by
krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but
must end in `.tab`.
pattern: "*tab"
- report:
type: file
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."