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Re-add the 'native' combined kaiju output

This commit is contained in:
James Fellows Yates 2023-02-16 14:02:13 +01:00
parent 4e818efe6d
commit 7dfcdd015b
4 changed files with 30 additions and 5 deletions

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@ -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'
}

View file

@ -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

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@ -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 ) {

View file

@ -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