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refactor: add warning when run_kraken2 is missing

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Moritz E. Beber 2022-10-17 17:16:21 +02:00
parent 563b34c9c3
commit fd8a0df2a6
1 changed files with 1 additions and 0 deletions
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workflows/taxprofiler.nf
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@ -41,6 +41,7 @@ if (params.longread_hostremoval_index ) { ch_longread_reference_index = fi
if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available." if (params.diamond_save_reads ) log.warn "[nf-core/taxprofiler] DIAMOND only allows output of a single format. As --diamond_save_reads supplied, only aligned reads in SAM format will be produced, no taxonomic profiles will be available."
if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT." if (params.run_malt && params.run_krona && !params.krona_taxonomy_directory) log.warn "[nf-core/taxprofiler] Krona can only be run on MALT output if path to Krona taxonomy database supplied to --krona_taxonomy_directory. Krona will not be executed in this run for MALT."
if (params.run_bracken && !params.run_kraken2) log.warn '[nf-core/taxprofiler] You are attempting to run Bracken without running kraken2. This is not possible! Please set --run_kraken2 as well.'
/* /*
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