Commit 2d1ca1b8 authored by Sander Bollen's avatar Sander Bollen
Browse files

fix dependency issues

parent bd6b308f
Pipeline #2622 failed with stages
in 4 minutes and 9 seconds
......@@ -469,7 +469,7 @@ rule genotype_gather_tbi:
input:
vcf = "multisample/genotyped.vcf.gz"
output:
tbi = "mulitsample/genotyped.vcf.gz.tbi"
tbi = "multisample/genotyped.vcf.gz.tbi"
singularity: "docker://quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
shell: "tabix -pvcf {input.vcf}"
......@@ -672,6 +672,7 @@ rule vtools_coverage:
"""Calculate coverage statistics per transcript"""
input:
gvcf="{sample}/vcf/{sample}.g.vcf.gz",
tbi = "{sample}/vcf/{sample}.g.vcf.gz.tbi",
ref=get_refflatpath
output:
tsv="{sample}/coverage/{ref}.coverages.tsv"
......@@ -685,7 +686,8 @@ rule vtools_coverage:
rule vcfstats:
"""Calculate vcf statistics"""
input:
vcf="multisample/genotyped.vcf.gz"
vcf="multisample/genotyped.vcf.gz",
tbi = "multisample/genotyped.vcf.gz.tbi"
output:
stats="multisample/vcfstats.json"
singularity: "docker://quay.io/biocontainers/vtools:1.0.0--py37h3010b51_0"
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment