Commit 1bac00d0 authored by van den Berg's avatar van den Berg
Browse files

Mark the scattered vcf outputs as temporary

parent 74dd7e6c
Pipeline #3523 failed with stages
in 1 minute and 52 seconds
......@@ -389,8 +389,8 @@ rule genotype_scatter:
tbi = "{sample}/vcf/{sample}.{chunk}.g.vcf.gz.tbi",
ref=REFERENCE
output:
vcf="{sample}/vcf/{sample}.{chunk}.vcf.gz",
vcf_tbi="{sample}/vcf/{sample}.{chunk}.vcf.gz.tbi"
vcf = temp("{sample}/vcf/{sample}.{chunk}.vcf.gz"),
vcf_tbi = temp("{sample}/vcf/{sample}.{chunk}.vcf.gz.tbi")
wildcard_constraints:
chunk="[0-9]+"
singularity: containers["gatk"]
......@@ -405,10 +405,17 @@ def aggregate_vcf(wildcards):
i=glob_wildcards(os.path.join(checkpoint_output, 'scatter-{i}.bed')).i)
def aggregate_vcf_tbi(wildcards):
checkpoint_output = checkpoints.scatterregions.get(**wildcards).output[0]
return expand("{{sample}}/vcf/{{sample}}.{i}.vcf.gz.tbi",
i=glob_wildcards(os.path.join(checkpoint_output, 'scatter-{i}.bed')).i)
rule genotype_gather:
"""Gather all genotyping VCFs"""
input:
vcfs = aggregate_vcf
vcfs = aggregate_vcf,
tbi = aggregate_vcf_tbi
output:
vcf = "{sample}/vcf/{sample}.vcf.gz"
singularity: containers["bcftools"]
......
......@@ -104,3 +104,7 @@
- "GT:AD:DP:GQ:PL:SB\t0/1:72,73,0:145:99:1909,0,1872,2125,2089,4214:35,37,36,37"
- "chrM\t16560\t.\tC\t<NON_REF>\t.\t.\tEND=16569\tGT:DP:GQ:MIN_DP:PL\t0/0:188:0:180:0,0,0"
- path: "micro/vcf/micro.0.vcf.gz"
should_exist: false
- path: "micro/vcf/micro.0.vcf.gz.tbi"
should_exist: false
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