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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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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -808,7 +808,7 @@ 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 ? { "${meta.db_params} --output-all -m lca --output-unclassified" } : { "${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}/" },
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