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Try Moritz's trick, assuming validate_db_rows already checks for tool name validity

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James A. Fellows Yates 2023-01-24 12:43:34 +01:00 committed by GitHub
parent 4df3409f4a
commit 6eafcc6499
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1 changed files with 3 additions and 11 deletions
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14
subworkflows/local/db_check.nf
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@ -39,18 +39,10 @@ workflow DB_CHECK {
skip: true skip: true
} }
//Filter the channel to run untar on DBs of tools actually using // 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() ch_input_untar = ch_dbs_for_untar.untar.dump()
.filter { .filter {
params.run_bracken && it[0]['tool'] == 'bracken' || params["run_${it[0]['tool']}"]
params.run_centrifuge && it[0]['tool'] == 'centrifuge' ||
params.run_diamond && it[0]['tool'] == 'diamond' ||
params.run_kaiju && it[0]['tool'] == 'kaiju' ||
params.run_kraken2 && it[0]['tool'] == 'kraken2' ||
params.run_krakenuniq && it [0]['tool'] == 'krakenuniq' ||
params.run_malt && it[0]['tool'] == 'malt' ||
params.run_metaphlan3 && it[0]['tool'] == 'metaphlan3' ||
params.run_motus && it[0]['tool'] == 'motus'
} }
UNTAR (ch_input_untar) UNTAR (ch_input_untar)
ch_versions = ch_versions.mix(UNTAR.out.versions.first()) ch_versions = ch_versions.mix(UNTAR.out.versions.first())