From 59b525b529bbc258917dd9bcaad78d8a32c554b8 Mon Sep 17 00:00:00 2001 From: Vadym Date: Wed, 8 Nov 2023 10:31:34 +0100 Subject: [PATCH] Fix python directive --- .../snakemake_rules/variant_calling/gens_preprocessing.rule | 4 ++-- CHANGELOG.rst | 1 + 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule b/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule index d96f085df..e2b32534f 100644 --- a/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule +++ b/BALSAMIC/snakemake_rules/variant_calling/gens_preprocessing.rule @@ -90,8 +90,8 @@ rule gens_preprocessing: "Formatting output for GENS for sample: {params.sample}." shell: """ -{params.gens_preprocessing} -s {params.sequencing_type} -o {output.gens_baf_bed} calculate-bafs --vcf-file-path {input.gnomad_af5_vcf} -{params.gens_preprocessing} -s {params.sequencing_type} -o {output.gens_cov_bed} create-coverage-regions --normalised-coverage-path {input.denoised_cr} +python {params.gens_preprocessing} -s {params.sequencing_type} -o {output.gens_baf_bed} calculate-bafs --vcf-file-path {input.gnomad_af5_vcf} +python {params.gens_preprocessing} -s {params.sequencing_type} -o {output.gens_cov_bed} create-coverage-regions --normalised-coverage-path {input.denoised_cr} """ rule finalize_gens_outputfiles: diff --git a/CHANGELOG.rst b/CHANGELOG.rst index e31b5a356..c79d70d42 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -82,6 +82,7 @@ Fixed: * CNVpytor container, fixing numpy version https://github.com/Clinical-Genomics/BALSAMIC/pull/1273 * QC workflow store https://github.com/Clinical-Genomics/BALSAMIC/pull/1295 * MultiQC rule missing input files https://github.com/Clinical-Genomics/BALSAMIC/pull/1321 +* `gens_preprocessing` rule missing python directive https://github.com/Clinical-Genomics/BALSAMIC/pull/1322 Removed: ^^^^^^^^