From 6eafcc6499ebefc076fe1363b2047fced3b8a033 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 24 Jan 2023 12:43:34 +0100 Subject: [PATCH] Try Moritz's trick, assuming validate_db_rows already checks for tool name validity --- subworkflows/local/db_check.nf | 14 +++----------- 1 file changed, 3 insertions(+), 11 deletions(-) diff --git a/subworkflows/local/db_check.nf b/subworkflows/local/db_check.nf index f5cdf2c..7490b72 100644 --- a/subworkflows/local/db_check.nf +++ b/subworkflows/local/db_check.nf @@ -39,18 +39,10 @@ workflow DB_CHECK { 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() - .filter { - params.run_bracken && it[0]['tool'] == 'bracken' || - 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' + .filter { + params["run_${it[0]['tool']}"] } UNTAR (ch_input_untar) ch_versions = ch_versions.mix(UNTAR.out.versions.first())