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Remove taxonomy parameter from taxpasta
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parent
211b5f3a68
commit
04bc978ef6
3 changed files with 1 additions and 12 deletions
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@ -543,12 +543,7 @@ process {
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}
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}
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withName: TAXPASTA_MERGE {
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withName: TAXPASTA_MERGE {
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ext.args = {
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ext.args = { "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}" }
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[
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"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
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params.standardisation_taxpasta_addtaxonomy ? "-p" : ""
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].join(' ').trim()
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}
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publishDir = [
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publishDir = [
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path: { "${params.outdir}/taxpasta/" },
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path: { "${params.outdir}/taxpasta/" },
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mode: params.publish_dir_mode,
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mode: params.publish_dir_mode,
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@ -156,7 +156,6 @@ params {
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// profile standardisation
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// profile standardisation
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run_profile_standardisation = false
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run_profile_standardisation = false
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standardisation_taxpasta_addtaxonomy = false
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standardisation_taxpasta_format = 'tsv'
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standardisation_taxpasta_format = 'tsv'
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standardisation_motus_generatebiom = false
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standardisation_motus_generatebiom = false
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}
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}
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@ -516,11 +516,6 @@
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"fa_icon": "fas fa-file",
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"fa_icon": "fas fa-file",
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"description": "The desired output format.",
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"description": "The desired output format.",
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"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
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"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
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},
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"standardisation_taxpasta_addtaxonomy": {
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"type": "boolean",
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"description": "The path to a directory containing taxdump files, typically from NCBI.",
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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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}
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}
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},
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},
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"fa_icon": "fas fa-chart-line"
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"fa_icon": "fas fa-chart-line"
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