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Rename taxpasta parameters and remove samplesheet parameter

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sofstam 2023-02-17 14:47:29 +01:00
parent 604df56fdb
commit f0aa89cb87
3 changed files with 16 additions and 23 deletions
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7
conf/modules.config
View file

@ -534,7 +534,7 @@ process {
} }
withName: MOTUS_MERGE { withName: MOTUS_MERGE {
ext.args = { params.generate_biom_output ? "-B" : "" } ext.args = { params.standardisation_motus_generatebiom ? "-B" : "" }
ext.prefix = { "motus_${meta.id}_combined_reports" } ext.prefix = { "motus_${meta.id}_combined_reports" }
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/" }, path: { "${params.outdir}/motus/" },
@ -545,9 +545,8 @@ process {
withName: TAXPASTA_MERGE { withName: TAXPASTA_MERGE {
ext.args = { ext.args = {
[ [
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.taxpasta_standardisation_format}", "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_taxonomy ? "-p" : "", params.standardisation_taxpasta_addtaxonomy ? "-p" : ""
params.taxpasta_add_samplesheet ? "-s" :""
].join(' ').trim() ].join(' ').trim()
} }
publishDir = [ publishDir = [

7
nextflow.config
View file

@ -156,10 +156,9 @@ params {
// profile standardisation // profile standardisation
run_profile_standardisation = false run_profile_standardisation = false
taxpasta_add_taxonomy = false standardisation_taxpasta_addtaxonomy = false
taxpasta_add_samplesheet = false standardisation_taxpasta_format = 'tsv'
taxpasta_standardisation_format = 'tsv' standardisation_motus_generatebiom = false
generate_biom_output = false
} }
// Load base.config by default for all pipelines // Load base.config by default for all pipelines

25
nextflow_schema.json
View file

@ -491,11 +491,11 @@
"description": "Turn on standardisation of taxon tables across profilers", "description": "Turn on standardisation of taxon tables across profilers",
"help_text": "Turns on standardisation of output OTU tables across all tools; each into a TSV format following the following scheme:\n\n|TAXON | SAMPLE_A | SAMPLE_B |\n|-------------|----------------|-----------------|\n| taxon_a | 32 | 123 |\n| taxon_b | 1 | 5 |\n\nThis currently only is generated for mOTUs." "help_text": "Turns on standardisation of output OTU tables across all tools; each into a TSV format following the following scheme:\n\n|TAXON | SAMPLE_A | SAMPLE_B |\n|-------------|----------------|-----------------|\n| taxon_a | 32 | 123 |\n| taxon_b | 1 | 5 |\n\nThis currently only is generated for mOTUs."
}, },
"generate_biom_output": { "standardisation_motus_generatebiom": {
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turn on generation of BIOM output (currently only applies to mOTUs)", "description": "Turn on generation of BIOM output (currently only applies to mOTUs)",
"help_text": "Turn on the saving of the taxonomic output in BIOM format (`.biom`) in the results directory of your pipeline run, instead of the default TSV format.\n\nNote this file is from the output of the `motus merge` command.\n\n> Modifies tool parameter(s):\n> - `-B -o`" "help_text": "Turn on the saving of the taxonomic output in BIOM format (`.biom`) in the results directory of your pipeline run, instead of the default TSV format.\\n\\nNote this file is from the output of the `motus merge` command.\\n\\n> Modifies tool parameter(s):\\n> - `-B -o`"
}, },
"run_krona": { "run_krona": {
"type": "boolean", "type": "boolean",
@ -510,22 +510,17 @@
"description": "Specify path to krona taxonomy directories (required for MALT krona plots)", "description": "Specify path to krona taxonomy directories (required for MALT krona plots)",
"help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package." "help_text": "Specify a path to a Krona taxonomy database directory (i.e. a directory containing a krona generated `.tab` file).\n\nThis is only required for generating Krona plots of MALT output.\n\nNote this taxonomy database must be downloaded and generated with the `updateTaxonomy.sh` script from the krona-tools package."
}, },
"taxpasta_add_taxonomy": { "standardisation_taxpasta_format": {
"type": "boolean",
"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."
},
"taxpasta_add_samplesheet": {
"type": "boolean",
"description": "A table with with two columns, one for the sample and one for the taxonomic profile.",
"help_text": "If this option is provided, any arguments are ignored."
},
"taxpasta_standardisation_format": {
"type": "string", "type": "string",
"default": "tsv", "default": "tsv",
"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"]
"fa_icon": "fas fa-file" },
"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"