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Merge pull request #205 from genomic-medicine-sweden/optional_untar

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Optional untar on dbs
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Sofia Stamouli 2022-12-23 13:14:04 +01:00 committed by GitHub
commit 59fd676ab3
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1 changed files with 7 additions and 5 deletions
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12
subworkflows/local/db_check.nf
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@ -2,7 +2,7 @@
// Check input samplesheet and get read channels // Check input samplesheet and get read channels
// //
include { UNTAR } from '../../modules/nf-core/untar/main' include { UNTAR } from '../../modules/nf-core/untar/main'
workflow DB_CHECK { workflow DB_CHECK {
take: take:
@ -10,6 +10,8 @@ workflow DB_CHECK {
main: main:
ch_versions = Channel.empty() ch_versions = Channel.empty()
ch_dbs_for_untar = Channel.empty()
ch_final_dbs = Channel.empty()
// special check to check _between_ rows, for which we must group rows together // special check to check _between_ rows, for which we must group rows together
// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first // note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
@ -37,11 +39,11 @@ workflow DB_CHECK {
skip: true skip: true
} }
// TODO Filter to only run UNTAR on DBs of tools actually using? //Filter the channel to run untar on DBs of tools actually using
// TODO make optional whether to save ch_input_untar = ch_dbs_for_untar.untar.dump()
UNTAR ( ch_dbs_for_untar.untar ) .filter { params.run_kraken2 && it[0]['tool'] == 'kraken2' || params.run_centrifuge && it[0]['tool'] == 'centrifuge' || params.run_bracken && it[0]['tool'] == 'bracken' || params.run_kaiju && it[0]['tool'] == 'kaiju' || params.run_krakenuniq && it [0]['tool'] == 'krakenuniq' || params.run_malt && it[0]['tool'] == 'malt' || params.run_metaphlan3 && it[0]['tool'] == 'metaphlan3' }
UNTAR (ch_input_untar)
ch_versions = ch_versions.mix(UNTAR.out.versions.first()) ch_versions = ch_versions.mix(UNTAR.out.versions.first())
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar ) ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
emit: emit: