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fix: snakefmt on eval
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famosab committed Mar 27, 2024
1 parent d5cd840 commit 502cea4
Showing 1 changed file with 7 additions and 5 deletions.
12 changes: 7 additions & 5 deletions workflow/rules/eval.smk
Original file line number Diff line number Diff line change
Expand Up @@ -29,22 +29,24 @@ rule add_genotype_field:
# bcftools convert makes sure that input for vcf-genotype-annotator is in vcf format
"vcf-genotype-annotator <(bcftools convert -Ov {input}) {params} 0/1 -o {output} &> {log} || bcftools view {input} -Oz > {output}"


rule add_format_field:
input:
"resources/variants/{genome}/all.truth.norm.bcf"
input:
"resources/variants/{genome}/all.truth.norm.bcf",
output:
"resources/variants/{genome}/all.truth.format-added.vcf.gz"
"resources/variants/{genome}/all.truth.format-added.vcf.gz",
log:
"logs/add_format_field/{genome}.log"
"logs/add_format_field/{genome}.log",
conda:
"../envs/vatools.yaml"
"../envs/vatools.yaml"
shell:
# TODO: Optional - Check first if FORMAT field is present for example with
# TODO: bcftools view -h out.vcf.gz | grep FORMAT oder bcftools query -l all.bcf
# bcftools convert makes sure that input for vcf-genotype-annotator is in vcf format
# adds FORMAT field with GT field and sample name 'truth'
"vcf-genotype-annotator <(bcftools convert -Ov {input}) truth 0/1 -o {output} &> {log}"


rule remove_non_pass:
input:
get_callset,
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