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Merge pull request #240 from nf-core/move-kaiju2table

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Move kaiju2table to profiling
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James A. Fellows Yates 2023-02-16 15:03:59 +01:00 committed by GitHub
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3 changed files with 22 additions and 6 deletions
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11
conf/modules.config
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@ -486,7 +486,16 @@ 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}/" },
mode: params.publish_dir_mode,
pattern: '*.{txt}'
]
}
withName: '.*STANDARDISATION_PROFILES:KAIJU_KAIJU2TABLE' {
ext.prefix = { "kaiju_${meta.id}_combined_reports" }
publishDir = [
path: { "${params.outdir}/kaiju/" },

10
docs/output.md
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@ -332,18 +332,20 @@ 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`)
- `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 `_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

5
subworkflows/local/profiling.nf
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@ -11,6 +11,7 @@ include { CENTRIFUGE_CENTRIFUGE } from '../../modules/nf-core/ce
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'
@ -271,6 +272,10 @@ workflow PROFILING {
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_profiles = ch_raw_profiles.mix( KAIJU_KAIJU2TABLE.out.summary )
}
if ( params.run_diamond ) {