From 51755f26d410c90be104b3b3c6ff45cb2d4c57a0 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Wed, 18 Jan 2023 13:53:26 +0100 Subject: [PATCH] make linter happy --- snappy_pipeline/workflows/sv_calling_wgs/Snakefile | 4 +++- snappy_pipeline/workflows/sv_calling_wgs/__init__.py | 4 +--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/snappy_pipeline/workflows/sv_calling_wgs/Snakefile b/snappy_pipeline/workflows/sv_calling_wgs/Snakefile index 572df7540..5c3749658 100644 --- a/snappy_pipeline/workflows/sv_calling_wgs/Snakefile +++ b/snappy_pipeline/workflows/sv_calling_wgs/Snakefile @@ -14,8 +14,10 @@ RE_BETWEEN_DOTS = r"[^.\.]+" # Configuration =============================================================== + configfile: "config.yaml" + # Expand "$ref" JSON pointers in configuration (also works for YAML) config, lookup_paths, config_paths = expand_ref("config.yaml", config) @@ -284,7 +286,7 @@ rule sv_calling_wgs_popdel_reorder_vcf: log: **wf.get_log_file("popdel", "reorder_vcf"), wrapper: - wf.wrapper_path("popdel/reorder_vcf") + wf.wrapper_path("popdel/reorder_vcf") # Run Melt -------------------------------------------------------------------- diff --git a/snappy_pipeline/workflows/sv_calling_wgs/__init__.py b/snappy_pipeline/workflows/sv_calling_wgs/__init__.py index 128cdb55e..50a0ca0d2 100644 --- a/snappy_pipeline/workflows/sv_calling_wgs/__init__.py +++ b/snappy_pipeline/workflows/sv_calling_wgs/__init__.py @@ -250,9 +250,7 @@ def _get_output_files_reorder_vcf(self): yield from work_files.items() yield "output_links", [ re.sub(r"^work/", "output/", work_path) - for work_path in chain( - work_files.values(), self.get_log_file("reorder_vcf").values() - ) + for work_path in chain(work_files.values(), self.get_log_file("reorder_vcf").values()) ] def get_ped_members(self, wildcards):