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Remove taxonomy parameter from taxpasta

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This commit is contained in:
sofstam 2023-02-20 11:56:06 +01:00
parent 211b5f3a68
commit 04bc978ef6
3 changed files with 1 additions and 12 deletions
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7
conf/modules.config
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@ -543,12 +543,7 @@ process {
} }
withName: TAXPASTA_MERGE { withName: TAXPASTA_MERGE {
ext.args = { ext.args = { "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}" }
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.standardisation_taxpasta_addtaxonomy ? "-p" : ""
].join(' ').trim()
}
publishDir = [ publishDir = [
path: { "${params.outdir}/taxpasta/" }, path: { "${params.outdir}/taxpasta/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

1
nextflow.config
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@ -156,7 +156,6 @@ params {
// profile standardisation // profile standardisation
run_profile_standardisation = false run_profile_standardisation = false
standardisation_taxpasta_addtaxonomy = false
standardisation_taxpasta_format = 'tsv' standardisation_taxpasta_format = 'tsv'
standardisation_motus_generatebiom = false standardisation_motus_generatebiom = false
} }

5
nextflow_schema.json
View file

@ -516,11 +516,6 @@
"fa_icon": "fas fa-file", "fa_icon": "fas fa-file",
"description": "The desired output format.", "description": "The desired output format.",
"enum": ["tsv", "csv", "arrow", "parquet", "biom"] "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
},
"standardisation_taxpasta_addtaxonomy": {
"type": "boolean",
"description": "The path to a directory containing taxdump files, typically from NCBI.",
"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
} }
}, },
"fa_icon": "fas fa-chart-line" "fa_icon": "fas fa-chart-line"