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Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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James A. Fellows Yates 2023-02-09 08:01:52 +01:00 committed by GitHub
parent b3837cce5b
commit 70eb84b8d5
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3 changed files with 2 additions and 4 deletions
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1
conf/modules.config
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@ -359,6 +359,7 @@ process {
} }
withName: BRACKEN_BRACKEN { withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
ext.args = { "${meta.db_params}" } ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" } ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.bracken" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.bracken" }
publishDir = [ publishDir = [

2
docs/usage.md
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@ -103,7 +103,7 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_database/
motus,db_mOTU,,/<path>/<to>/motus/motus_database/ motus,db_mOTU,,/<path>/<to>/motus/motus_database/
``` ```
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. 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.
Column specifications are as follows: Column specifications are as follows:

3
subworkflows/local/profiling.nf
View file

@ -141,7 +141,6 @@ workflow PROFILING {
[ meta, reads, db_meta_new, db ] [ meta, reads, db_meta_new, db ]
} }
.dump(tag: "ch_input_for_kraken2_after")
.multiMap { .multiMap {
it -> it ->
reads: [ it[0] + it[2], it[1] ] reads: [ it[0] + it[2], it[1] ]
@ -184,7 +183,6 @@ workflow PROFILING {
ch_input_for_bracken = ch_kraken2_output ch_input_for_bracken = ch_kraken2_output
.map { meta, report -> [meta['db_name'], meta, report] } .map { meta, report -> [meta['db_name'], meta, report] }
.combine(ch_bracken_databases, by: 0) .combine(ch_bracken_databases, by: 0)
.dump(tag: "ch_input_for_bracken_b4")
.map { .map {
key, meta, reads, db_meta, db -> key, meta, reads, db_meta, db ->
@ -208,7 +206,6 @@ workflow PROFILING {
[ key, meta, reads, db_meta_new, db ] [ key, meta, reads, db_meta_new, db ]
} }
.dump(tag: "ch_input_for_bracken_after")
.multiMap { key, meta, report, db_meta, db -> .multiMap { key, meta, report, db_meta, db ->
report: [meta + db_meta, report] report: [meta + db_meta, report]
db: db db: db