From 577d27042353208dbe4c65293b9bfd4f29735f1c Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Fri, 17 Mar 2023 10:14:40 +0100 Subject: [PATCH 1/2] Deactivate saving of reads and other large files for full tests --- conf/test_full.config | 74 +++++++++++++++++++++---------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index e8bcb31..e540df7 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -19,52 +19,52 @@ params { // Genome references hostremoval_reference = 'ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/819/615/GCA_000819615.1_ViralProj14015/GCA_000819615.1_ViralProj14015_genomic.fna.gz' - save_preprocessed_reads = true + save_preprocessed_reads = false - perform_shortread_qc = true - shortread_qc_mergepairs = true - perform_shortread_complexityfilter = true - save_complexityfiltered_reads = true + perform_shortread_qc = true + shortread_qc_mergepairs = true + perform_shortread_complexityfilter = false + save_complexityfiltered_reads = false - perform_longread_qc = true - perform_shortread_hostremoval = true - perform_longread_hostremoval = true - save_hostremoval_index = true - save_hostremoval_bam = true - save_hostremoval_unmapped = true + perform_longread_qc = true + perform_shortread_hostremoval = true + perform_longread_hostremoval = true + save_hostremoval_index = false + save_hostremoval_bam = false + save_hostremoval_unmapped = false - perform_runmerging = true - save_runmerged_reads = true + perform_runmerging = true + save_runmerged_reads = false - run_centrifuge = true - centrifuge_save_reads = true + run_centrifuge = true + centrifuge_save_reads = false - run_diamond = true + run_diamond = true - run_kaiju = true + run_kaiju = true - run_kraken2 = true - kraken2_save_reads = true - kraken2_save_readclassification = true - kraken2_save_minimizers = true + run_kraken2 = true + kraken2_save_reads = false + kraken2_save_readclassification = false + kraken2_save_minimizers = false - run_krakenuniq = true - krakenuniq_save_reads = true - krakenuniq_save_readclassifications = true + run_krakenuniq = true + krakenuniq_save_reads = false + krakenuniq_save_readclassifications = false - run_bracken = true - - run_malt = true - malt_save_reads = true - malt_generate_megansummary = true - - run_metaphlan3 = true - - run_motus = true - motus_save_mgc_read_counts = true - - run_profile_standardisation = true - run_krona = true + run_bracken = true + + run_malt = true + malt_save_reads = false + malt_generate_megansummary = true + + run_metaphlan3 = true + + run_motus = true + motus_save_mgc_read_counts = true + + run_profile_standardisation = true + run_krona = true } cleanup = true From 142ff2f09943c603fb39e87ce13700d72cbf07aa Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 17 Mar 2023 10:26:38 +0100 Subject: [PATCH 2/2] Apply suggestions from code review --- conf/test_full.config | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index e540df7..e0673e0 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -53,16 +53,15 @@ params { krakenuniq_save_readclassifications = false run_bracken = true - run_malt = true malt_save_reads = false malt_generate_megansummary = true - + run_metaphlan3 = true - + run_motus = true motus_save_mgc_read_counts = true - + run_profile_standardisation = true run_krona = true }