From 90a5668007b84a5ece6fa85b2385514c4cd7790d Mon Sep 17 00:00:00 2001 From: sofstam Date: Fri, 17 Feb 2023 15:38:36 +0100 Subject: [PATCH] run_malt false in test and add text in output.md --- conf/test.config | 4 ++-- docs/output.md | 2 ++ subworkflows/local/standardisation_profiles.nf | 1 - 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/conf/test.config b/conf/test.config index 925987e..c80533a 100644 --- a/conf/test.config +++ b/conf/test.config @@ -25,7 +25,7 @@ params { perform_shortread_qc = true perform_longread_qc = true shortread_qc_mergepairs = true - perform_shortread_complexityfilter = false + perform_shortread_complexityfilter = true perform_shortread_hostremoval = true perform_longread_hostremoval = true perform_runmerging = true @@ -33,7 +33,7 @@ params { run_kaiju = true run_kraken2 = true run_bracken = true - run_malt = true + run_malt = false run_metaphlan3 = true run_centrifuge = true run_diamond = true diff --git a/docs/output.md b/docs/output.md index 9a7518d..1e39576 100644 --- a/docs/output.md +++ b/docs/output.md @@ -463,6 +463,8 @@ The following report files are used for the taxpasta step: - MetaPhlAn3: `_profile.txt` Taxpasta uses the `relative_abundance` column multiplied with a fixed number to yield an integer for the standardised profile. - mOTUs: `.out` Taxpasta uses the `read_count` column for the standardised profile. +Please aware the outputs of each tool's standardised profile _may not_ be directly comparable between each tool. Some may report raw read counts, whereas others may report abundance information. Please always refer to the list above, for which information is used for each tool. + ### MultiQC
diff --git a/subworkflows/local/standardisation_profiles.nf b/subworkflows/local/standardisation_profiles.nf index d928263..de58622 100644 --- a/subworkflows/local/standardisation_profiles.nf +++ b/subworkflows/local/standardisation_profiles.nf @@ -141,7 +141,6 @@ workflow STANDARDISATION_PROFILES { ch_multiqc_files = ch_multiqc_files.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.txt ) ch_versions = ch_versions.mix( METAPHLAN3_MERGEMETAPHLANTABLES.out.versions ) - // mOTUs // mOTUs has a 'single' database, and cannot create custom ones.