Commit af8cdafa authored by Sander Bollen's avatar Sander Bollen
Browse files

copy bai files

parent ca449a4c
......@@ -122,6 +122,8 @@ def metrics(do_metrics=True):
rule all:
input:
combined=out_path("multisample/genotyped.vcf.gz"),
bais=expand(out_path("{sample}/bams/{sample}.markdup.bam.bai"),
sample=SAMPLES),
stats=metrics()
......@@ -226,6 +228,7 @@ rule markdup:
tmp = ancient(out_path("tmp"))
output:
bam = out_path("{sample}/bams/{sample}.markdup.bam"),
bai = out_path("{sample}/bams/{sample}.markdup.bai"),
metrics = out_path("{sample}/bams/{sample}.markdup.metrics")
conda: "envs/picard.yml"
shell: "picard MarkDuplicates CREATE_INDEX=TRUE TMP_DIR={input.tmp} "
......@@ -233,6 +236,14 @@ rule markdup:
"METRICS_FILE={output.metrics} "
"MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=500"
rule bai:
"""Copy bai files as some genome browsers can only .bam.bai files"""
input:
bai = out_path("{sample}/bams/{sample}.markdup.bai")
output:
bai = out_path("{sample}/bams/{sample}.markdup.bam.bai")
shell: "cp {input.bai} {output.bai}"
rule baserecal:
"""Base recalibrated BAM files"""
input:
......
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment