diff --git a/workflow/rules/eval.smk b/workflow/rules/eval.smk index e05d239..b7eabb7 100644 --- a/workflow/rules/eval.smk +++ b/workflow/rules/eval.smk @@ -29,15 +29,16 @@ 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 @@ -45,6 +46,7 @@ rule add_format_field: # 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,