Fix python directive

Clinical-Genomics · Nov 8, 2023 · 59b525b · 59b525b
1 parent 33f1531
commit 59b525b
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diff --git 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
@@ -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:
 ^^^^^^^^