Commit 84e685d4 authored by van den Berg's avatar van den Berg
Browse files

Add input constraint

parent 745aff96
......@@ -343,6 +343,8 @@ rule gvcf_scatter:
output:
gvcf=temp("{sample}/vcf/{sample}.{chunk}.g.vcf.gz"),
gvcf_tbi=temp("{sample}/vcf/{sample}.{chunk}.g.vcf.gz.tbi")
wildcard_constraints:
chunk="[0-9]+"
singularity: containers["gatk"]
shell: "java -jar -Xmx4G -XX:ParallelGCThreads=1 /usr/GenomeAnalysisTK.jar "
"-T HaplotypeCaller -ERC GVCF -I "
......@@ -378,8 +380,10 @@ rule genotype_scatter:
tbi = "{sample}/vcf/{sample}.{chunk}.g.vcf.gz.tbi",
ref=REFERENCE
output:
vcf="{sample}/vcf/{sample}.genotype.{chunk}.vcf.gz",
vcf_tbi="{sample}/vcf/{sample}.genotype.{chunk}.vcf.gz.tbi"
vcf="{sample}/vcf/{sample}.{chunk}.vcf.gz",
vcf_tbi="{sample}/vcf/{sample}.{chunk}.vcf.gz.tbi"
wildcard_constraints:
chunk="[0-9]+"
singularity: containers["gatk"]
shell: "java -jar -Xmx15G -XX:ParallelGCThreads=1 /usr/GenomeAnalysisTK.jar -T "
"GenotypeGVCFs -R {input.ref} "
......@@ -389,7 +393,7 @@ rule genotype_scatter:
rule genotype_gather:
"""Gather all genotyping VCFs"""
input:
vcfs = "{sample}/vcf/{sample}.genotype.{chunk}.vcf.gz",
vcfs = "{sample}/vcf/{sample}.{chunk}.vcf.gz",
output:
vcf = "{sample}/vcf/{sample}.vcf.gz"
singularity: containers["bcftools"]
......
......@@ -58,3 +58,25 @@
- path: "micro/vcf/micro.1.g.vcf.gz"
- path: "scatter/scatter-1.bed"
- path: "scatter/scatter-13.bed"
- name: test-new-scatter-vcf
tags:
- integration
- scatter
command: >
snakemake
--use-singularity
--singularity-prefix /tmp/singularity
--singularity-args ' --cleanenv --bind /tmp'
--jobs 1 -w 120
-r -p -s Snakefile
micro/vcf/micro.1.vcf.gz
--config
REFERENCE=tests/data/ref.fa
DBSNP=tests/data/database.vcf.gz
KNOWN_SITES=tests/data/database.vcf.gz
SAMPLE_CONFIG=tests/data/sample_config.json
files:
- path: "scatter/scatter-1.bed"
- path: "scatter/scatter-13.bed"
- path: "micro/vcf/micro.1.vcf.gz"
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