From 335be556c98e1fc515116f0dbdc736eb193c282f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 16 Dec 2024 08:52:22 +0100 Subject: [PATCH 1/3] docs: link to scenario catalog --- config/README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/config/README.md b/config/README.md index 5fd15e3d..e6636173 100644 --- a/config/README.md +++ b/config/README.md @@ -36,6 +36,7 @@ Missing values can be specified by empty columns or by writing `NA`. Lines can b Varlociraptor supports integrated uncertainty aware calling and filtering of variants for arbitrary scenarios. These are defined as so-called scenarios, via a [variant calling grammar](https://varlociraptor.github.io/docs/calling#generic-variant-calling). * For each group, a scenario is rendered via [YTE](https://yte-template-engine.github.io). * Therefore, edit the template scenario (`scenario.yaml`) according to your needs. The sample sheet is available for YTE rendering as a pandas data frame in the variable `samples`. This allows to customize the scenario according to the contents of the sample sheet. You can therefore add additional columns to the sample sheet (e.g. purity) and access them in the scenario template, in order to pass the information to Varlociraptor. +* Example scenarios for various use cases can be found in the [scenario catalog](https://varlociraptor.github.io/varlociraptor-scenarios). # Primer trimming From 349523920f72120801509fb6aee244b31bfeab73 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 16 Dec 2024 08:54:59 +0100 Subject: [PATCH 2/3] docs: explain fdr control mode --- config/config.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/config/config.yaml b/config/config.yaml index 009a06ef..f1deaf49 100644 --- a/config/config.yaml +++ b/config/config.yaml @@ -153,7 +153,9 @@ calling: expression: "ANN['SYMBOL'] in AUX['super_interesting_genes']" fdr-control: threshold: 0.05 - # denote FDR control mode, see https://varlociraptor.github.io/docs/filtering + # Denote FDR control mode. + # The default (local-smart) is recommended because it provides the most realistic and intuitive results. + # See see https://varlociraptor.github.io/docs/filtering for details. mode: local-smart events: # Add any number of events here to filter for. From 0cf0fa833787a9d37a17195cfa342374625a165b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Felix=20M=C3=B6lder?= Date: Wed, 8 Jan 2025 12:13:34 +0100 Subject: [PATCH 3/3] fix: cache ref data (#348) * fix: cache ref data * Update ref.smk --- workflow/rules/ref.smk | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk index 6d7d4725..5299e150 100644 --- a/workflow/rules/ref.smk +++ b/workflow/rules/ref.smk @@ -150,11 +150,12 @@ rule get_vep_plugins: rule get_pangenome_haplotypes: output: - temp(f"{pangenome_prefix}.vcf.gz"), + f"{pangenome_prefix}.vcf.gz", params: url=config["ref"]["pangenome"]["vcf"], log: "logs/pangenome/haplotypes.log", + cache: "omit-software" shell: "curl -o {output} {params.url} 2> {log}" @@ -163,11 +164,12 @@ rule rename_haplotype_contigs: input: f"{pangenome_prefix}.vcf.gz", output: - temp("resources/haplotype_contigs_renamed.tsv"), + "resources/haplotype_contigs_renamed.tsv", params: expressions=config["ref"]["pangenome"].get("rename_expressions", []), log: "logs/pangenome/chrom_replacement.log", + cache: "omit-software" conda: "../envs/pysam.yaml" script: @@ -179,9 +181,10 @@ rule rename_haplotype_chroms: vcf="resources/{pangenome}.vcf.gz", tsv="resources/haplotype_contigs_renamed.tsv", output: - temp("resources/{pangenome}.renamed.vcf.gz"), + "resources/{pangenome}.renamed.vcf.gz", log: "logs/pangenome/{pangenome}_renamed.log", + cache: "omit-software" conda: "../envs/bcftools.yaml" shell: