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Code Issues Releases Packages Activity

Rename taxonomy argument

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sofstam 2023-02-24 13:04:38 +01:00
parent 5a6fcf1f42
commit 5dc3cbc278
3 changed files with 3 additions and 3 deletions
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2
conf/modules.config
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@ -546,7 +546,7 @@ process {
ext.args = { ext.args = {
[ [
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}", "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_taxonomy ? "--taxonomy" : "", params.taxpasta_taxonomy_files ? "--taxonomy" : "",
].join(' ').trim() ].join(' ').trim()
} }
publishDir = [ publishDir = [

2
nextflow.config
View file

@ -157,7 +157,7 @@ params {
// profile standardisation // profile standardisation
run_profile_standardisation = false run_profile_standardisation = false
standardisation_taxpasta_format = 'tsv' standardisation_taxpasta_format = 'tsv'
taxpasta_add_taxonomy = false taxpasta_taxonomy_files = false
standardisation_motus_generatebiom = false standardisation_motus_generatebiom = false
} }

2
nextflow_schema.json
View file

@ -517,7 +517,7 @@
"description": "The desired output format.", "description": "The desired output format.",
"enum": ["tsv", "csv", "arrow", "parquet", "biom"] "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
}, },
"taxpasta_add_taxonomy": { "taxpasta_taxonomy_files": {
"type": "boolean", "type": "boolean",
"description": "The path to a directory containing taxdump files.", "description": "The path to a directory containing taxdump files.",
"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional." "help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."