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Merged
aweich merged 2 commits into from
Mar 4, 2025
Merged

Cmod #5

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cbcc989
forgot to add before
Mar 4, 2025
7fe2e37
Merge pull request #4 from aweich/main
aweich Mar 4, 2025
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3 changes: 1 addition & 2 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -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))

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2 changes: 1 addition & 1 deletion workflow/rules/functional_genomics.smk
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Expand Up @@ -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)
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