millironx/taxprofiler
1
0
Fork 0
mirror of https://github.com/MillironX/taxprofiler.git synced 2024-11-22 00:26:03 +00:00
Code Issues Releases Packages Activity

Apply suggestions from code review

Browse source 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
This commit is contained in:
James A. Fellows Yates 2023-02-09 08:01:52 +01:00 committed by GitHub
parent b3837cce5b
commit 70eb84b8d5
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
3 changed files with 2 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

1
conf/modules.config
View file

@ -359,6 +359,7 @@ process {
}
withName: BRACKEN_BRACKEN {
errorStrategy = 'ignore'
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" }
publishDir = [

2
docs/usage.md
View file

@ -103,7 +103,7 @@ metaphlan3,db1,,/<path>/<to>/metaphlan3/metaphlan_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:

3
subworkflows/local/profiling.nf
View file

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