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Get fixed Krona module and add Krona taxonomy to test profile

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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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1
conf/test.config
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@ -38,6 +38,7 @@ params {
run_centrifuge = true run_centrifuge = true
run_diamond = true run_diamond = true
run_krona = 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 malt_save_reads = true
kraken2_save_reads = true kraken2_save_reads = true
centrifuge_save_reads = true centrifuge_save_reads = true

2
modules.json
View file

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

9
modules/nf-core/modules/krona/ktimporttaxonomy/main.nf generated
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@ -10,7 +10,7 @@ process KRONA_KTIMPORTTAXONOMY {
input: input:
tuple val(meta), path(report) tuple val(meta), path(report)
path taxonomy path taxonomy, stageAs: 'taxonomy.tab'
output: output:
tuple val(meta), path ('*.html'), emit: html tuple val(meta), path ('*.html'), emit: html
@ -24,10 +24,13 @@ process KRONA_KTIMPORTTAXONOMY {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. 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 \\ ktImportTaxonomy \\
$args \\ $args \\
-o ${prefix}.html \\ -o ${prefix}.html \\
-tax $taxonomy \\ -tax \$TAXONOMY/ \\
$report $report
cat <<-END_VERSIONS > versions.yml cat <<-END_VERSIONS > versions.yml
@ -35,4 +38,4 @@ process KRONA_KTIMPORTTAXONOMY {
krona: $VERSION krona: $VERSION
END_VERSIONS END_VERSIONS
""" """
} }

7
modules/nf-core/modules/krona/ktimporttaxonomy/meta.yml generated
View file

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