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include krakenuniq in profiling subworkflow

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This commit is contained in:
Mahwash Jamy 2022-10-25 09:45:05 +00:00
parent 36e101a78b
commit 86ca71cfd4
2 changed files with 22 additions and 0 deletions
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4
modules.json
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@ -89,6 +89,10 @@
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
}, },
"krakenuniq/preloadedkrakenuniq": {
"branch": "master",
"git_sha": "13b9d4854593c03e5e25e8a8f47462542c2c0dd4"
},
"krona/ktimporttaxonomy": { "krona/ktimporttaxonomy": {
"branch": "master", "branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905" "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"

18
subworkflows/local/profiling.nf
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@ -11,6 +11,7 @@ include { METAPHLAN3_METAPHLAN3 } from '../../modules/nf-core/me
include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main' include { KAIJU_KAIJU } from '../../modules/nf-core/kaiju/kaiju/main'
include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main' include { DIAMOND_BLASTX } from '../../modules/nf-core/diamond/blastx/main'
include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main' include { MOTUS_PROFILE } from '../../modules/nf-core/motus/profile/main'
include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from '../../modules/nf-core/krakenuniq/preloadedkrakenuniq/main'
workflow PROFILING { workflow PROFILING {
take: take:
@ -45,6 +46,7 @@ workflow PROFILING {
kaiju: it[2]['tool'] == 'kaiju' kaiju: it[2]['tool'] == 'kaiju'
diamond: it[2]['tool'] == 'diamond' diamond: it[2]['tool'] == 'diamond'
motus: it[2]['tool'] == 'motus' motus: it[2]['tool'] == 'motus'
krakenuniq: it[2]['tool'] == 'krakenuniq'
unknown: true unknown: true
} }
@ -228,6 +230,22 @@ workflow PROFILING {
ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log ) ch_multiqc_files = ch_multiqc_files.mix( MOTUS_PROFILE.out.log )
} }
if ( params.run_krakenuniq ) {
ch_input_for_krakenuniq = ch_input_for_profiling.krakenuniq
.multiMap {
it ->
reads: [ it[0] + it[2], it[1] ]
db: it[3]
}
KRAKENUNIQ_PRELOADEDKRAKENUNIQ ( ch_input_for_krakenuniq.reads, ch_input_for_krakenuniq.db, params.krakenuniq_save_reads, params.krakenuniq_save_readclassification )
ch_multiqc_files = ch_multiqc_files.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
ch_versions = ch_versions.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.versions.first() )
ch_raw_classifications = ch_raw_classifications.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.classified_assignment )
ch_raw_profiles = ch_raw_profiles.mix( KRAKENUNIQ_PRELOADEDKRAKENUNIQ.out.report )
}
emit: emit:
classifications = ch_raw_classifications classifications = ch_raw_classifications
profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom profiles = ch_raw_profiles // channel: [ val(meta), [ reads ] ] - should be text files or biom