From a43821a6ce45bae2fe8c2b7847e392d4e552820a Mon Sep 17 00:00:00 2001 From: jvfe Date: Wed, 24 Jul 2024 20:48:05 -0300 Subject: [PATCH] docs: Update param docs --- docs/params.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/params.md b/docs/params.md index 928da88..b3529b8 100644 --- a/docs/params.md +++ b/docs/params.md @@ -48,6 +48,7 @@ Parameters for the annotation subworkflow | `min_qcover` | Minimum coverage of each match for filtering | `number` | 0.6 | | `skip_profile_creation` | Skip annotation feature profile creation | `boolean` | | | `feature_profile_columns` | Columns to include in the feature profile | `string` | mobsuite,rgi,cazy,vfdb,iceberg,bacmet | +| `upset_plot_columns` | Columns to use for making Upset plots of genome features | `string` | | ## Phylogenomics @@ -71,7 +72,7 @@ Parameters for the lineage subworkflow | `poppunk_model` | Which PopPunk model to use (bgmm, dbscan, refine, threshold or lineage) | `string` | | | `run_poppunk_qc` | Whether to run the QC step for PopPunk | `boolean` | | | `enable_subsetting` | Enable subsetting workflow based on genome similarity | `boolean` | | -| `core_similarity` | Similarity threshold for core genomes | `number` | 99.99 | +| `core_similarity` | Similarity threshold for core genomes | `number` | 99.9 | | `accessory_similarity` | Similarity threshold for accessory genes | `number` | 99 | ## Gene Order