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3 changed files with 3 additions and 3 deletions
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@ -546,7 +546,7 @@ process {
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ext.args = {
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[
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"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
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params.taxpasta_taxonomy_files ? "--taxonomy" : "",
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params.taxpasta_taxonomy_dir ? "--taxonomy" ${params.taxpasta_taxonomy_dir}" : "",
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].join(' ').trim()
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}
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publishDir = [
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@ -157,7 +157,7 @@ params {
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// profile standardisation
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run_profile_standardisation = false
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standardisation_taxpasta_format = 'tsv'
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taxpasta_taxonomy_files = false
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taxpasta_taxonomy_dir = false
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standardisation_motus_generatebiom = false
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}
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@ -517,7 +517,7 @@
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"description": "The desired output format.",
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"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
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},
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"taxpasta_taxonomy_files": {
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"taxpasta_taxonomy_dir": {
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"type": "boolean",
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"description": "The path to a directory containing taxdump files.",
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"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
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