From 4cf693d228144bd9da546598fedff4fa27fcb376 Mon Sep 17 00:00:00 2001 From: BiancaStoecker Date: Thu, 10 Apr 2025 13:24:31 +0000 Subject: [PATCH 1/2] fix: add .get() for optional values in config instead of dictionary access. --- workflow/rules/common.smk | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index b45b183..18adf4d 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -208,9 +208,9 @@ def get_callset(wildcards): vcf = callset["path"] if get_somatic_status(wildcards): return "results/normalized-variants/{callset}.gt-added.vcf.gz" - elif callset.get("rename-contigs", False) != False: + elif callset.get("rename-contigs", False) == True: return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz" - elif callset["genome-build"] == "grch37": + elif callset.get("genome-build", "grch38") == "grch37": return "results/normalized-variants/{callset}.lifted.vcf.gz" elif isinstance(vcf, dict): return "results/merge-callsets/{callset}.merged.vcf.gz" @@ -221,9 +221,9 @@ def get_callset(wildcards): def get_callset_correct_contigs(wildcards): callset = config["variant-calls"][wildcards.callset] vcf = callset["path"] - if "rename-contigs" in callset: + if callset.get("rename-contigs", False): return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz" - elif callset["genome-build"] == "grch37": + elif callset.get("genome-build", "grch38") == "grch37": return "results/normalized-variants/{callset}.lifted.vcf.gz" elif isinstance(vcf, dict): return "results/merge-callsets/{callset}.merged.vcf.gz" @@ -234,9 +234,9 @@ def get_callset_correct_contigs(wildcards): def get_callset_correct_contigs_liftover(wildcards): callset = config["variant-calls"][wildcards.callset] vcf = callset["path"] - if callset["genome-build"] == "grch37": + if callset.get("genome-build", "grch38") == "grch37": return "results/normalized-variants/{callset}.lifted.vcf.gz" - elif callset.get("rename-contigs", False) != False: + elif callset.get("rename-contigs", False): return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz" elif isinstance(vcf, dict): return "results/merge-callsets/{callset}.merged.vcf.gz" @@ -388,17 +388,17 @@ def get_test_regions(wildcards): def get_rename_contig_file(wildcards): - if config["variant-calls"][wildcards.callset][ - "genome-build" - ] == "grch37" and config["variant-calls"][wildcards.callset].get( + if config["variant-calls"][wildcards.callset].get( + "genome-build", "grch38" + ) == "grch37" and config["variant-calls"][wildcards.callset].get( "rename-contigs", False ): return workflow.source_path( "../resources/rename-contigs/grch37_ucsc2ensembl.txt" ) - if config["variant-calls"][wildcards.callset][ - "genome-build" - ] == "grch38" and config["variant-calls"][wildcards.callset].get( + if config["variant-calls"][wildcards.callset].get( + "genome-build", "grch38" + ) == "grch38" and config["variant-calls"][wildcards.callset].get( "rename-contigs", False ): return workflow.source_path( From c6a6b7f8c279f71185686ab6375833b84740dafc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bianca=20St=C3=B6cker?= Date: Fri, 11 Apr 2025 10:39:16 +0200 Subject: [PATCH 2/2] fix: remove superfluous == True MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- workflow/rules/common.smk | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk index 18adf4d..031de8c 100644 --- a/workflow/rules/common.smk +++ b/workflow/rules/common.smk @@ -208,7 +208,7 @@ def get_callset(wildcards): vcf = callset["path"] if get_somatic_status(wildcards): return "results/normalized-variants/{callset}.gt-added.vcf.gz" - elif callset.get("rename-contigs", False) == True: + elif callset.get("rename-contigs", False): return "results/normalized-variants/{callset}.replaced-contigs.vcf.gz" elif callset.get("genome-build", "grch38") == "grch37": return "results/normalized-variants/{callset}.lifted.vcf.gz"