From 000f4789047a9f3bbdd4ac85fc7c09daa15a72fe Mon Sep 17 00:00:00 2001 From: Till Hartmann Date: Thu, 23 May 2024 16:42:15 +0200 Subject: [PATCH] doc comment for filter_list in pydantic model for somatic_variant_filtration --- .../somatic_variant_filtration/model.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/snappy_pipeline/workflows/somatic_variant_filtration/model.py b/snappy_pipeline/workflows/somatic_variant_filtration/model.py index 127a58b8d..6f0fc9bd9 100644 --- a/snappy_pipeline/workflows/somatic_variant_filtration/model.py +++ b/snappy_pipeline/workflows/somatic_variant_filtration/model.py @@ -106,6 +106,23 @@ class SomaticVariantFiltration(SnappyStepModel): eb_filter: Annotated[EbfilterSet | None, Field(deprecated="use filter_list instead")] = None filter_list: list[Filter] = [] + """ + Available filters + dkfz: {} # Not parametrisable + ebfilter: + ebfilter_threshold: 2.4 + shuffle_seed: 1 + panel_of_normals_size: 25 + min_mapq: 20 + min_baseq: 15 + bcftools: + include: "" # Expression to be used in bcftools view --include + exclude: "" # Expression to be used in bcftools view --exclude + regions: + path_bed: REQUIRED # Bed file of regions to be considered (variants outside are filtered out) + protected: + path_bed: REQUIRED # Bed file of regions that should not be filtered out at all. + """ @model_validator(mode="after") def ensure_filter_list_is_configured_correctly(self: Self) -> Self: