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sofstam 2023-02-27 10:15:42 +01:00
parent 78d7001bea
commit 2f0c68a833
4 changed files with 31 additions and 1 deletions
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4
conf/modules.config
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@ -547,6 +547,10 @@ process {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_taxonomy_dir ? "--taxonomy ${params.taxpasta_taxonomy_dir}" : "",
params.taxpasta_add_name ? "--add-name" : "",
params.taxpasta_add_rank ? "--add-rank" : "",
params.taxpasta_add_lineage ? "--add-lineage" : "",
params.taxpasta_add_idlineage ? "--add-id-lineage" : "",
].join(' ').trim()
}
publishDir = [

2
docs/output.md
View file

@ -449,7 +449,7 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
</details>
By enabling the parameter `--taxonomy` and giving the path to a directory containing taxdump files, the taxon name, the taxon rank and the taxon's entire lineage can be added in the output. Those should be configured through `ext.args` by respectively using the parameters `--add-name`, `--add-rank` and `--add-lineage`.
By enabling the parameter `--taxonomy` and giving the path to a directory containing taxdump files, the taxon name, the taxon rank, the taxon's entire lineage including taxon names and the taxon's entire lineage including taxon identifiers can be added in the output. Those should be configured through `ext.args` by respectively using the parameters `--add-name`, `--add-rank`, `--add-lineage` and `--add-id-lineage`.
These files will likely be the most useful files for the comparison of differences in classification between different tools or building consensuses, with the caveat they have slightly less information than the actual output from each tool (which may have non-standard information e.g. taxonomic rank, percentage of hits, abundance estimations).

4
nextflow.config
View file

@ -158,6 +158,10 @@ params {
run_profile_standardisation = false
standardisation_taxpasta_format = 'tsv'
taxpasta_taxonomy_dir = false
taxpasta_add_name = false
taxpasta_add_rank = false
taxpasta_add_lineage = false
taxpasta_add_idlineage = false
standardisation_motus_generatebiom = false
}

22
nextflow_schema.json
View file

@ -521,6 +521,28 @@
"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_name": {
"type": "string",
"default": "false",
"description": "Add the taxon name to the output."
},
"taxpasta_add_rank": {
"type": "string",
"default": "false",
"description": "Add the taxon rank to the output."
},
"taxpasta_add_lineage": {
"type": "string",
"default": "false",
"description": "Add the taxon's entire lineage to the output.",
"help_text": "These are taxon names separated by semi-colons. "
},
"taxpasta_add_idlineage": {
"type": "string",
"default": "false",
"description": "Add the taxon's entire lineage to the output.",
"help_text": "These are taxon identifiers separated by semi-colons. "
}
},
"fa_icon": "fas fa-chart-line"