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Apply suggestions from code review
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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3 changed files with 2 additions and 4 deletions
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@ -359,6 +359,7 @@ process {
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}
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withName: BRACKEN_BRACKEN {
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errorStrategy = 'ignore'
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ext.args = { "${meta.db_params}" }
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ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
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publishDir = [
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@ -103,7 +103,7 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
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motus,db_mOTU,,/<path>/<to>/motus/motus_database/
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```
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For Bracken, if you wish to supply amy parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
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For Bracken, if you wish to supply any parameters to either the Kraken or Bracken step you **must** have a _semi-colon_ `;` list as in `db_params`. This is to allow to specify the Kraken2 parameters before, and Bracken parameters after the `;` as Bracken is a two step process. This is particularly important if you supply a Bracken database with a non-default read length parameter. If you do not have any parameters to specify, you can leave this as empty.
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Column specifications are as follows:
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@ -141,7 +141,6 @@ workflow PROFILING {
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[ meta, reads, db_meta_new, db ]
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}
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.dump(tag: "ch_input_for_kraken2_after")
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.multiMap {
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it ->
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reads: [ it[0] + it[2], it[1] ]
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@ -184,7 +183,6 @@ workflow PROFILING {
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ch_input_for_bracken = ch_kraken2_output
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.map { meta, report -> [meta['db_name'], meta, report] }
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.combine(ch_bracken_databases, by: 0)
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.dump(tag: "ch_input_for_bracken_b4")
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.map {
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key, meta, reads, db_meta, db ->
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@ -208,7 +206,6 @@ workflow PROFILING {
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[ key, meta, reads, db_meta_new, db ]
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}
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.dump(tag: "ch_input_for_bracken_after")
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.multiMap { key, meta, report, db_meta, db ->
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report: [meta + db_meta, report]
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db: db
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