Commit a6207a25 authored by Sander Bollen's avatar Sander Bollen
Browse files

metrics in all

parent 27582b11
......@@ -80,9 +80,36 @@ def sample_gender(wildcards):
return sam.get("gender", "null")
def metrics(do_metrics=True):
if not do_metrics:
return ""
mnum = expand(out_path("{sample}/bams/{sample}.mapped.num"),
sample=SAMPLES)
mbnum = expand(out_path("{sample}/bams/{sample}.mapped.basenum"),
sample=SAMPLES)
unum = expand(out_path("{sample}/bams/{sample}.unique.num"),
sample=SAMPLES)
ubnum = expand(out_path("{sample}/bams/{sample}.usable.basenum"),
sample=SAMPLES)
fqcr = expand(out_path("{sample}/pre_process/raw_fastqc/.done.txt"),
sample=SAMPLES)
fqcm = expand(out_path("{sample}/pre_process/merged_fastqc/.done.txt"),
sample=SAMPLES)
fqcp = expand(out_path("{sample}/pre_process/postqc_fastqc/.done.txt"),
sample=SAMPLES)
fnumpre = expand(out_path("{sample}/pre_process/{sample}.preqc_count.json"),
sample=SAMPLES)
fnumpos = expand(out_path("{sample}/pre_process/{sample}.preqc_count.json"),
sample=SAMPLES)
return mnum + mbnum + unum + ubnum + fqcr + fqcm + fqcp + fnumpre + fnumpos
rule all:
input:
combined=out_path("multisample/genotyped.vcf.gz")
combined=out_path("multisample/genotyped.vcf.gz"),
stats=metrics()
rule genome:
input: REFERENCE
......
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