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correct parameter to use lca for multiple matches in ganon classify #523

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merged 4 commits into from
Sep 11, 2024
Merged

correct parameter to use lca for multiple matches in ganon classify #523

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af8bc72
replace output-lca into -m lca in ganon classify
LilyAnderssonLee Sep 10, 2024
9500726
Drop unnecesary ganon parameter (should come via db_params) and patte…
jfy133 Sep 11, 2024
5bc5716
Update output docs
jfy133 Sep 11, 2024
8bf5833
Update parameter docs
jfy133 Sep 11, 2024
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4 changes: 2 additions & 2 deletions conf/modules.config
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Expand Up @@ -808,12 +808,12 @@ process {

withName: GANON_CLASSIFY {
tag = {"${meta.db_name}|${meta.id}"}
ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-lca --output-unclassified" } : { "${meta.db_params}" }
ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-unclassified" } : { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.ganon" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon" }
publishDir = [
path: { "${params.outdir}/ganon/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{tre,rep,lca,all,unc,log}'
pattern: '*.{tre,rep,one,all,unc,log}'
]
}

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6 changes: 3 additions & 3 deletions docs/output.md
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Expand Up @@ -618,9 +618,9 @@ The main taxonomic classification file from KMCP is the `*kmcp.profile` which is
- `<sample_id>_report.tre`: output of `ganon report` containing taxonomic classifications with possible formatting and/or filtering depending on options specified.
- `<sample_id>`.tre: output of `ganon classify` containing raw taxonomic classifications and abundance estimations with no additional formatting or filtering.
- `<sample_id>`.rep: 'raw' report of counts against each taxon.
- `<sample_id>`.all: per-read summary of all hits of each reads.
- `<sample_id>`.lca: per-read summary of the best single hit after LCA for each read.
- `<sample_id>`.unc: list of read IDs with no hits.
- `<sample_id>`.all: per-read summary of all hits of each read. Only generated if `--ganon_save_readclassifications` specified.
- `<sample_id>`.one: per-read summary of the best single hit after the selection by the user specified multiple match method for each read. Only generated if `--ganon_save_readclassifications` specified.
- `<sample_id>`.unc: list of read IDs with no hits. Only generated if `--ganon_save_readclassifications` specified.
- `<sample_id>`.log: the stdout console messages printed by `ganon classify`, containing some classification summary information

- `ganon_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by `ganon table`)
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -589,7 +589,7 @@
"type": "boolean",
"description": "Turn on saving of ganon per-read taxonomic assignment file(s).",
"fa_icon": "fas fa-save",
"help_text": "Saves `.lca`, `.all`, and `.unc` text files that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic assignment that the read received.\n\n> Modifies tool parameter(s):\n- ganon classify: `--output-all --output-lca --output-unclassified`"
"help_text": "Saves `.one`, `.all`, and `.unc` text files that contains a list of each read that had a taxonomic assignment, with information on specific taxonomic assignment that the read received.\n\n> Modifies tool parameter(s):\n- ganon classify: `--output-all --output-unclassified`"
},
"ganon_report_type": {
"type": "string",
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