From cbcc98924702e14391ea66280ca536578f77b003 Mon Sep 17 00:00:00 2001 From: weichan <@weichan> Date: Tue, 4 Mar 2025 10:17:06 +0100 Subject: [PATCH] forgot to add before --- workflow/Snakefile | 3 +-- workflow/rules/functional_genomics.smk | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/workflow/Snakefile b/workflow/Snakefile index 3b791d2..f309a52 100644 --- a/workflow/Snakefile +++ b/workflow/Snakefile @@ -31,8 +31,7 @@ if "functional_genomics" in config: import VIS_functional_genomics_helper_functions as vhf_fg include: config["functional_genomics"] conditional_output.append(expand(f"{outdir}/final/functional_genomics/Functional_distances_to_Insertions_{{sample}}.bed", sample=SAMPLES)) - conditional_output.append(expand(f"{outdir}/final/functional_genomics/Functional_distances_to_Insertions_{{sample}}.bed", sample=SAMPLES)) - conditional_output.append(expand(f"{outdir}/intermediate/localization/annotation/Annotation_{{annotation}}_Insertions_{{sample}}.bed", + conditional_output.append(expand(f"{outdir}/intermediate/functional_genomics/Annotation_{{annotation}}_Insertions_{{sample}}.bed", annotation=[k.replace("annotate_", "") for k in config if k.startswith("annotate_")], sample=SAMPLES)) diff --git a/workflow/rules/functional_genomics.smk b/workflow/rules/functional_genomics.smk index 4b11aee..a699bc9 100644 --- a/workflow/rules/functional_genomics.smk +++ b/workflow/rules/functional_genomics.smk @@ -46,7 +46,7 @@ rule annotation_overlap_insertion: log: log=f"{outdir}/intermediate/log/functional_genomics/annotation_overlap_insertion/{{sample}}.log" output: - **{k.replace("annotate_", ""): f"{outdir}/intermediate/localization/annotation/Annotation_{k.replace('annotate_', '')}_Insertions_{{sample}}.bed" + **{k.replace("annotate_", ""): f"{outdir}/intermediate/functional_genomics/Annotation_{k.replace('annotate_', '')}_Insertions_{{sample}}.bed" for k in config if k.startswith("annotate_")} run: vhf_fg.run_bedtools_intersect(input.insertions_bed, output, log.log, params.annotation_files)