Commit ef4bf0f0 authored by Sander Bollen's avatar Sander Bollen
Browse files

fix syntax errors

parent ac58a0c1
......@@ -177,18 +177,14 @@ def metrics(do_metrics=True):
if not do_metrics:
return ""
fqcr = expand("{sample}/pre_process/raw_fastqc/.done.txt",
sample=SAMPLES)
fqcm = expand("{sample}/pre_process/merged_fastqc/{sample}.merged_R1_fastqc.zip",
sample=SAMPLES)
fqcp = expand("{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip",
sample=SAMPLES)
fqcr = expand("{sample}/pre_process/raw_fastqc/.done.txt", sample=SAMPLES)
fqcm = expand("{sample}/pre_process/merged_fastqc/{sample}.merged_R1_fastqc.zip", sample=SAMPLES)
fqcp = expand("{sample}/pre_process/postqc_fastqc/{sample}.cutadapt_R1_fastqc.zip", sample=SAMPLES)
if len(REFFLATS) >= 1:
coverage_stats = expand("{sample}/coverage/{ref}.coverages.tsv",
sample=SAMPLES, ref=BASE_REFFLATS)
coverage_stats = expand("{sample}/coverage/{ref}.coverages.tsv", sample=SAMPLES, ref=BASE_REFFLATS)
else:
coverage_stats = []
stats = "stats.json")
stats = "stats.json"
return fqcr + fqcm + fqcp + coverage_stats + [stats]
......@@ -196,10 +192,8 @@ rule all:
input:
combined="multisample/genotyped.vcf.gz",
report="multiqc_report/multiqc_report.html",
bais=expand("{sample}/bams/{sample}.markdup.bam.bai",
sample=SAMPLES),
vcfs=expand("{sample}/vcf/{sample}_single.vcf.gz",
sample=SAMPLES),
bais=expand("{sample}/bams/{sample}.markdup.bam.bai",sample=SAMPLES),
vcfs=expand("{sample}/vcf/{sample}_single.vcf.gz",sample=SAMPLES),
stats=metrics()
......@@ -266,7 +260,7 @@ rule sickle:
output:
r1 = temp("{sample}/pre_process/{sample}.trimmed_R1.fastq"),
r2 = temp("{sample}/pre_process/{sample}.trimmed_R2.fastq"),
s = "{sample}/pre_process/{sample}.trimmed_singles.fastq",
s = "{sample}/pre_process/{sample}.trimmed_singles.fastq"
conda: "envs/sickle.yml"
shell: "sickle pe -f {input.r1} -r {input.r2} -t sanger -o {output.r1} "
"-p {output.r2} -s {output.s}"
......@@ -301,7 +295,7 @@ rule markdup:
"""Mark duplicates in BAM file"""
input:
bam = "{sample}/bams/{sample}.sorted.bam",
tmp = ancient("tmp"))
tmp = ancient("tmp")
output:
bam = "{sample}/bams/{sample}.markdup.bam",
bai = "{sample}/bams/{sample}.markdup.bai",
......@@ -364,15 +358,12 @@ rule gvcf_scatter:
rule gvcf_gather:
"""Gather all gvcf scatters"""
input:
gvcfs=expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz",
chunk=CHUNKS),
tbis=expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz.tbi",
chunk=CHUNKS),
gvcfs=expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz", chunk=CHUNKS),
tbis=expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz.tbi", chunk=CHUNKS),
ref=REFERENCE,
gatk=GATK
params:
gvcfs="' -V '".join(expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz",
chunk=CHUNKS))
gvcfs="' -V '".join(expand("{{sample}}/vcf/{{sample}}.{chunk}.part.vcf.gz", chunk=CHUNKS))
output:
gvcf="{sample}/vcf/{sample}.g.vcf.gz"
conda: "envs/gatk.yml"
......@@ -384,13 +375,11 @@ rule gvcf_gather:
rule genotype_scatter:
"""Run GATK's GenotypeGVCFs by chunk"""
input:
gvcfs = expand("{sample}/vcf/{sample}.g.vcf.gz",
sample=SAMPLES),
gvcfs = expand("{sample}/vcf/{sample}.g.vcf.gz", sample=SAMPLES),
ref=REFERENCE,
gatk=GATK
params:
li=" -V ".join(expand("{sample}/vcf/{sample}.g.vcf.gz",
sample=SAMPLES)),
li=" -V ".join(expand("{sample}/vcf/{sample}.g.vcf.gz", sample=SAMPLES)),
chunk="{chunk}"
output:
vcf=temp("multisample/genotype.{chunk}.part.vcf.gz"),
......@@ -403,15 +392,12 @@ rule genotype_scatter:
rule genotype_gather:
"""Gather all genotyping scatters"""
input:
vcfs=expand("multisample/genotype.{chunk}.part.vcf.gz",
chunk=CHUNKS),
tbis=expand("multisample/genotype.{chunk}.part.vcf.gz.tbi",
chunk=CHUNKS),
vcfs=expand("multisample/genotype.{chunk}.part.vcf.gz", chunk=CHUNKS),
tbis=expand("multisample/genotype.{chunk}.part.vcf.gz.tbi", chunk=CHUNKS),
ref=REFERENCE,
gatk=GATK
params:
vcfs="' -V '".join(expand("multisample/genotype.{chunk}.part.vcf.gz",
chunk=CHUNKS))
vcfs="' -V '".join(expand("multisample/genotype.{chunk}.part.vcf.gz", chunk=CHUNKS))
output:
combined="multisample/genotyped.vcf.gz"
conda: "envs/gatk.yml"
......@@ -622,8 +608,7 @@ if len(BASE_BEDS) >= 1:
unum="{sample}/bams/{sample}.unique.num",
ubnum="{sample}/bams/{sample}.usable.basenum",
fastqc="{sample}/pre_process/fastq_stats.json",
cov=expand("{{sample}}/coverage/{bed}.covstats.json",
bed=BASE_BEDS),
cov=expand("{{sample}}/coverage/{bed}.covstats.json", bed=BASE_BEDS),
colpy=colpy
params:
sample_name="{sample}",
......@@ -693,7 +678,7 @@ rule multiqc:
input:
stats="stats.tsv"
params:
odir="."),
odir=".",
rdir="multiqc_report"
output:
report="multiqc_report/multiqc_report.html"
......
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