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Merge pull request #219 from nf-core/allow-targz-motus [skip ci]

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Allow all tool's databases to be provided as `.tar.gz` files
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James A. Fellows Yates 2023-01-25 13:48:43 +01:00 committed by GitHub
commit 47efd193cb
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1 changed files with 6 additions and 3 deletions
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9
subworkflows/local/db_check.nf
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@ -39,9 +39,12 @@ workflow DB_CHECK {
skip: true
}
//Filter the channel to run untar on DBs of tools actually using
ch_input_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' }
// Filter the channel to untar only those databases for tools that are selected to be run by the user.
ch_input_untar = ch_dbs_for_untar.untar.dump()
.filter {
params["run_${it[0]['tool']}"]
}
UNTAR (ch_input_untar)
ch_versions = ch_versions.mix(UNTAR.out.versions.first())
ch_final_dbs = ch_dbs_for_untar.skip.mix( UNTAR.out.untar )