From 6b47739c1c59514ff5b5b5145a7d6b2bfde7f3bd Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 11 Jun 2024 16:40:49 +0200 Subject: [PATCH] Add nonpareil to testing --- conf/test.config | 55 ++++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 27 deletions(-) diff --git a/conf/test.config b/conf/test.config index 5af08d72..0c6d260d 100644 --- a/conf/test.config +++ b/conf/test.config @@ -20,33 +20,34 @@ params { max_time = '6.h' // Input data - input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' - databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' - perform_shortread_qc = true - perform_longread_qc = true - shortread_qc_mergepairs = true - perform_shortread_complexityfilter = true - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - perform_runmerging = true - hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' - run_kaiju = true - run_kraken2 = true - run_bracken = true - run_malt = false - run_metaphlan = true - run_centrifuge = true - run_diamond = true - run_krakenuniq = true - run_motus = false - run_ganon = true - run_krona = true - run_kmcp = true - krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab' - malt_save_reads = true - kraken2_save_reads = true - centrifuge_save_reads = true - run_profile_standardisation = true + input = params.pipelines_testdata_base_path + 'taxprofiler/samplesheet.csv' + databases = params.pipelines_testdata_base_path + 'taxprofiler/database_v1.1.csv' + perform_shortread_qc = true + perform_shortread_redundancyestimation = true + perform_longread_qc = true + shortread_qc_mergepairs = true + perform_shortread_complexityfilter = true + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + perform_runmerging = true + hostremoval_reference = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta' + run_kaiju = true + run_kraken2 = true + run_bracken = true + run_malt = false + run_metaphlan = true + run_centrifuge = true + run_diamond = true + run_krakenuniq = true + run_motus = false + run_ganon = true + run_krona = true + run_kmcp = true + krona_taxonomy_directory = params.pipelines_testdata_base_path + 'modules/data/genomics/sarscov2/metagenome/krona_taxonomy.tab' + malt_save_reads = true + kraken2_save_reads = true + centrifuge_save_reads = true + run_profile_standardisation = true } process {