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Optional untar on dbs
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parent
35b296e5fd
commit
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1 changed files with 7 additions and 5 deletions
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@ -2,7 +2,7 @@
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// Check input samplesheet and get read channels
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//
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include { UNTAR } from '../../modules/nf-core/untar/main'
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include { UNTAR } from '../../modules/nf-core/untar/main'
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workflow DB_CHECK {
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take:
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@ -10,6 +10,8 @@ workflow DB_CHECK {
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main:
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ch_versions = Channel.empty()
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ch_dbs_for_untar = Channel.empty()
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ch_final_dbs = Channel.empty()
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// special check to check _between_ rows, for which we must group rows together
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// note: this will run in parallel to within-row validity, but we can assume this will run faster thus will fail first
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@ -37,11 +39,11 @@ workflow DB_CHECK {
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skip: true
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}
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// TODO Filter to only run UNTAR on DBs of tools actually using?
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// TODO make optional whether to save
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UNTAR ( ch_dbs_for_untar.untar )
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//Filter the channel to run untar on DBs of tools actually using
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ch_input_untar = ch_dbs_for_untar.untar.dump()
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.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' }
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UNTAR (ch_input_untar)
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ch_versions = ch_versions.mix(UNTAR.out.versions.first())
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ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )
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emit:
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