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Move kaiju2table to profiling

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This commit is contained in:
James Fellows Yates 2023-02-16 13:39:05 +01:00
parent 21d9135b14
commit 79b4db9a34
4 changed files with 15 additions and 24 deletions
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4
conf/modules.config
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@ -487,9 +487,9 @@ process {
}
withName: KAIJU_KAIJU2TABLE {
ext.prefix = { "kaiju_${meta.id}_combined_reports" }
ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.kaijutable" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.kaijutable" }
publishDir = [
path: { "${params.outdir}/kaiju/" },
path: { "${params.outdir}/kaiju/${meta.db_name}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
]

9
docs/output.md
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@ -332,18 +332,19 @@ The main taxonomic classification files from Centrifuge are the `_combined_repor
### Kaiju
[Kaiju](https://github.com/bioinformatics-centre/kaiju) is a taxonomic classifier that finds maximum exact matches on the protein-level using the Burrows–Wheeler transform.
[Kaiju](https://github.com/bioinformatics-centre/kaiju) is a taxonomic classifier that finds maximum exact matches on the protein-level using the Burrows-Wheeler transform.
<details markdown="1">
<summary>Output files</summary>
- `kaiju`
- `<sample_id>.tsv`: A file that summarises the fraction abundance, taxonomic ID, number of reads and taxonomic names
- `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 summary file is the `*combined_reports.txt` file which summarises results across all samples. However if you wish to look at more precise information about each assignment, check the per-sample 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 `*kaijutable.txt` file which summarises hits across all treads. However if you wish to look at more precise information on a per-read bases `*tsv` file. The default taxonomic rank is `species`. You can provide a different one by updating the argument `--kaiju_taxon_rank`.
### DIAMOND

10
subworkflows/local/profiling.nf
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@ -5,12 +5,13 @@
include { MALT_RUN } from '../../modules/nf-core/malt/run/main'
include { MEGAN_RMA2INFO as MEGAN_RMA2INFO_TSV } from '../../modules/nf-core/megan/rma2info/main'
include { KRAKEN2_KRAKEN2 } from '../../modules/nf-core/kraken2/kraken2/main'
include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
include { KRAKEN2_STANDARD_REPORT } from '../../modules/local/kraken2_standard_report'
include { BRACKEN_BRACKEN } from '../../modules/nf-core/bracken/bracken/main'
include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/centrifuge/centrifuge/main'
include { CENTRIFUGE_KREPORT } from '../../modules/nf-core/centrifuge/kreport/main'
include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/metaphlan3/metaphlan3/main'
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { KAIJU_KAIJU2TABLE } from '../../modules/nf-core/kaiju/kaiju2table/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
@ -269,7 +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 )
}

16
subworkflows/local/standardisation_profiles.nf
View file

@ -3,7 +3,6 @@
//
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'
@ -79,21 +78,6 @@ 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