mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:03:09 +00:00
Re-add the 'native' combined kaiju output
This commit is contained in:
parent
4e818efe6d
commit
7dfcdd015b
4 changed files with 30 additions and 5 deletions
|
@ -486,7 +486,7 @@ process {
|
|||
ext.args = { "${meta.db_params}" }
|
||||
}
|
||||
|
||||
withName: KAIJU_KAIJU2TABLE {
|
||||
withName: '.*PROFILING:KAIJU_KAIJU2TABLE' {
|
||||
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
|
||||
|
@ -495,6 +495,15 @@ process {
|
|||
]
|
||||
}
|
||||
|
||||
withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' {
|
||||
ext.prefix = { "kaiju_${meta.id}_combined_reports" }
|
||||
publishDir = [
|
||||
path: { "${params.outdir}/kaiju/" },
|
||||
mode: params.publish_dir_mode,
|
||||
pattern: '*.{txt}'
|
||||
]
|
||||
}
|
||||
|
||||
withName: KAIJU_KAIJU2KRONA {
|
||||
ext.args = '-v -u'
|
||||
}
|
||||
|
|
|
@ -338,13 +338,14 @@ The main taxonomic classification files from Centrifuge are the `_combined_repor
|
|||
<summary>Output files</summary>
|
||||
|
||||
- `kaiju`
|
||||
- `kaiju_<db_name>_combined_reports.txt`: A combined profile of all samples aligned to a given database (as generated by kaiju2table)
|
||||
- `<db_name>/`
|
||||
- `<sample_id>_<db_name>.kaiju.tsv`: Raw output from Kaiju with taxonomic rank, read ID and taxonic ID
|
||||
- `<sample_id>_<db_name>.kaijutable.txt`: Summarised Kaiju output with fraction abundance, taxonomic ID, number of reads, and taxonomic names (as generated by `kaiju2table`)
|
||||
|
||||
</details>
|
||||
|
||||
The most useful summary file is the `*kaijutable.txt` file which summarises hits across all reads. However if you wish to look at more precise information on a per-read basis, see the `*tsv` file. The default taxonomic rank is `species`. You can provide a different one by updating the argument `--kaiju_taxon_rank`.
|
||||
The most useful summary file is the `_combined_reports.txt` file which summarises hits across all reads and samples. Separate per-sample versions summaries can be seen in `<db>/*.txt`. However if you wish to look at more precise information on a per-read basis, see the `*tsv` file. The default taxonomic rank is `species`. You can provide a different one by updating the argument `--kaiju_taxon_rank`.
|
||||
|
||||
### DIAMOND
|
||||
|
||||
|
|
|
@ -270,13 +270,12 @@ workflow PROFILING {
|
|||
|
||||
KAIJU_KAIJU ( ch_input_for_kaiju.reads, ch_input_for_kaiju.db)
|
||||
ch_versions = ch_versions.mix( KAIJU_KAIJU.out.versions.first() )
|
||||
ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU.out.results )
|
||||
|
||||
KAIJU_KAIJU2TABLE ( KAIJU_KAIJU.out.results, ch_input_for_kaiju.db, params.kaiju_taxon_rank)
|
||||
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
|
||||
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
ch_raw_classifications = ch_raw_classifications.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
|
||||
ch_raw_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
}
|
||||
|
||||
if ( params.run_diamond ) {
|
||||
|
|
|
@ -3,6 +3,7 @@
|
|||
//
|
||||
|
||||
include { BRACKEN_COMBINEBRACKENOUTPUTS } from '../../modules/nf-core/bracken/combinebrackenoutputs/main'
|
||||
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
|
||||
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_KRAKEN } from '../../modules/nf-core/krakentools/combinekreports/main'
|
||||
include { KRAKENTOOLS_COMBINEKREPORTS as KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE } from '../../modules/nf-core/krakentools/combinekreports/main'
|
||||
include { METAPHLAN3_MERGEMETAPHLANTABLES } from '../../modules/nf-core/metaphlan3/mergemetaphlantables/main'
|
||||
|
@ -78,6 +79,21 @@ workflow STANDARDISATION_PROFILES {
|
|||
ch_multiqc_files = ch_multiqc_files.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.txt )
|
||||
ch_versions = ch_versions.mix( KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE.out.versions )
|
||||
|
||||
// Kaiju
|
||||
|
||||
// Collect and replace id for db_name for prefix
|
||||
ch_profiles_for_kaiju = ch_input_classifications.kaiju
|
||||
.map { [it[0]['db_name'], it[1]] }
|
||||
.groupTuple()
|
||||
.map {
|
||||
[[id:it[0]], it[1]]
|
||||
}
|
||||
|
||||
KAIJU_KAIJU2TABLE ( ch_profiles_for_kaiju, ch_input_databases.kaiju.map{it[1]}, params.kaiju_taxon_rank)
|
||||
ch_standardised_tables = ch_standardised_tables.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
ch_multiqc_files = ch_multiqc_files.mix( KAIJU_KAIJU2TABLE.out.summary )
|
||||
ch_versions = ch_versions.mix( KAIJU_KAIJU2TABLE.out.versions )
|
||||
|
||||
// Kraken2
|
||||
|
||||
// Collect and replace id for db_name for prefix
|
||||
|
|
Loading…
Reference in a new issue