From 1857c9f9c71a2e22ca3825d11a78b10de1ed55f5 Mon Sep 17 00:00:00 2001
From: Sascha Meiers <meiers@embl.de>
Date: Sun, 28 Oct 2018 10:15:10 +0100
Subject: [PATCH] Make reference genome a parameter rather than an input file.
This avoids trouble within singularity, where input file existence cannot be
checked before the container has been loaded
---
Snakefile | 11 ++++++-----
1 file changed, 6 insertions(+), 5 deletions(-)
diff --git a/Snakefile b/Snakefile
index 6962d0e..32c56d0 100644
--- a/Snakefile
+++ b/Snakefile
@@ -892,14 +892,15 @@ rule haplotag_bams:
vcf='phased-snvs/{sample}/{windows}.{bpdens}.vcf.gz',
tbi='phased-snvs/{sample}/{windows}.{bpdens}.vcf.gz.tbi',
bam='bam/{sample}/selected/{bam}.bam',
- bai='bam/{sample}/selected/{bam}.bam.bai',
- ref = config["reference"],
+ bai='bam/{sample}/selected/{bam}.bam.bai'
output:
bam='haplotag/bam/{sample}/{windows}.{bpdens,selected_j[0-9\\.]+_s[0-9\\.]+_scedist[0-9\\.]+}/{bam}.bam',
log:
"log/haplotag_bams/{sample}/{windows}.{bpdens}/{bam}.log"
+ params:
+ ref = config["reference"]
shell:
- "whatshap haplotag -o {output.bam} -r {input.ref} {input.vcf} {input.bam} > {log} 2>{log}"
+ "whatshap haplotag -o {output.bam} -r {params.ref} {input.vcf} {input.bam} > {log} 2>{log}"
rule create_haplotag_segment_bed:
input:
@@ -989,17 +990,17 @@ rule regenotype_SNVs:
input:
bam = "snv_calls/{sample}/merged.bam",
bai = "snv_calls/{sample}/merged.bam.bai",
- fa = config["reference"],
sites = config["snv_sites_to_genotype"],
output:
vcf = "snv_genotyping/{sample}/{chrom,chr[0-9A-Z]+}.vcf"
log:
"log/snv_genotyping/{sample}/{chrom}.log"
params:
+ fa = config["reference"],
bcftools = config["bcftools"]
shell:
"""
- (freebayes -f {input.fa} -r {wildcards.chrom} -@ {input.sites} --only-use-input-alleles {input.bam} --genotype-qualities | {params.bcftools} view --exclude-uncalled --genotype het --types snps --include "QUAL>=10" - > {output.vcf}) 2> {log}
+ (freebayes -f {params.fa} -r {wildcards.chrom} -@ {input.sites} --only-use-input-alleles {input.bam} --genotype-qualities | {params.bcftools} view --exclude-uncalled --genotype het --types snps --include "QUAL>=10" - > {output.vcf}) 2> {log}
"""
rule merge_SNV_calls:
--
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