diff --git a/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml b/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml index ba0061ad3..41262cb7e 100644 --- a/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml +++ b/workflow/resources/datavzrd/variant-calls-template.datavzrd.yaml @@ -289,8 +289,10 @@ views: display-mode: hidden chromosome: display-mode: detail + end position: + display-mode: detail position: - display-mode: detail + display-mode: detail reference allele: display-mode: detail alternative allele: diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index dcbc80a86..9aee5b52c 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -1065,7 +1065,6 @@ def get_annotation_fields_for_tables(wildcards): "CANONICAL", "CLIN_SIG", "Consequence", - "EXON", "Feature", "Gene", "gnomADg_AF", @@ -1146,7 +1145,7 @@ def get_info_prob_fields_for_tables(wildcards, input): scenario = yaml.load(scenario_file, Loader=yaml.SafeLoader) events = list(scenario["events"].keys()) events += ["artifact", "absent"] - return [f"PROB_{e.upper()}" for e in events] + return events else: return [] @@ -1215,7 +1214,10 @@ def get_vembrane_config(wildcards, input): ## INFO fields holding varlociraptor probabilities info_prob_fields = get_info_prob_fields_for_tables(wildcards, input) append_items( - info_prob_fields, rename_info_fields, "INFO['{}']".format, "prob: {}".format + info_prob_fields, + rename_info_fields, + lambda x: f"INFO['PROB_{x.upper()}']", + "prob: {}".format, ) ## INFO fields relevant in fusion calling, only added for 'fusion' calling @@ -1240,6 +1242,10 @@ def get_vembrane_config(wildcards, input): "gnomADg_AF": { "name": "gnomad genome af", }, + "EXON": { + "name": "exon", + "expr": "ANN['EXON'].raw", + }, "SpliceAI_pred_DS_AG": { "name": "spliceai acceptor gain", }, @@ -1263,7 +1269,6 @@ def get_vembrane_config(wildcards, input): "ANN['{}']".format, lambda x: x.lower(), ) - # determine a stable sort order, to avoid implicit assumptions about field # order; downstream scripts split-call-tables.py and # join_fusion_partner.py will remove columns they respectively don't need @@ -1283,7 +1288,7 @@ def get_vembrane_config(wildcards, input): "ANN['Consequence']", "ANN['CLIN_SIG']", "ANN['gnomADg_AF']", - "ANN['EXON']", + "ANN['EXON'].raw", "ANN['REVEL']", # variants only, split-call-tables.py will select the column with the # highest score and will put it in the same place @@ -1414,7 +1419,7 @@ def get_primer_extra(wc, input): min_primer_len = get_shortest_primer_length(input.reads) # Check if shortest primer is below default values if min_primer_len < 32: - extra += f" -T {min_primer_len-2}" + extra += f" -T {min_primer_len - 2}" if min_primer_len < 19: extra += f" -k {min_primer_len}" return extra diff --git a/workflow/rules/plugins.smk b/workflow/rules/plugins.smk index 34d4558e9..728e6fc87 100644 --- a/workflow/rules/plugins.smk +++ b/workflow/rules/plugins.smk @@ -6,7 +6,7 @@ rule download_revel: conda: "../envs/curl.yaml" shell: - "curl https://rothsj06.dmz.hpc.mssm.edu/revel-v1.3_all_chromosomes.zip -o {output} &> {log}" + "curl https://zenodo.org/records/7072866/files/revel-v1.3_all_chromosomes.zip -o {output} &> {log}" rule process_revel_scores: