Commit bb0f1582 authored by van den Berg's avatar van den Berg
Browse files

Switch to chunked-scatter instead of biopet

parent fb607603
......@@ -179,7 +179,7 @@ rule baserecal:
checkpoint scatterregions:
"""Scatter the reference genome"""
input:
ref = config["reference"],
ref = config["reference"] + '.fai',
output:
directory("scatter")
params:
......@@ -187,14 +187,16 @@ checkpoint scatterregions:
log:
"log/scatterregions.log"
container:
containers["biopet-scatterregions"]
containers["chunked-scatter"]
resources:
mem_mb = lambda wildcards, attempt: attempt * 10000
shell:
"mkdir -p {output} && "
"biopet-scatterregions -Xmx24G "
"--referenceFasta {input.ref} --scatterSize {params.size} "
"--outputDir scatter 2> {log}"
"scatter-regions "
"--scatter-size {params.size} "
"--split-contigs "
"--prefix {output}/scatter- "
"{input.ref} 2> {log}"
rule gvcf_scatter:
"""Run HaplotypeCaller in GVCF mode by chunk"""
......
......@@ -6,8 +6,8 @@ import os
containers = {
'bcftools': 'docker://quay.io/biocontainers/bcftools:1.9--ha228f0b_4',
'bedtools-2.26-python-2.7': 'docker://quay.io/biocontainers/mulled-v2-3251e6c49d800268f0bc575f28045ab4e69475a6:4ce073b219b6dabb79d154762a9b67728c357edb-0',
'biopet-scatterregions': 'docker://quay.io/biocontainers/biopet-scatterregions:0.2--0',
'bwa-0.7.17-samtools-1.10': 'docker://quay.io/biocontainers/mulled-v2-ad317f19f5881324e963f6a6d464d696a2825ab6:c59b7a73c87a9fe81737d5d628e10a3b5807f453-0',
'chunked-scatter': 'docker://quay.io/biocontainers/chunked-scatter:1.0.0--py_0',
'cutadapt': 'docker://quay.io/biocontainers/cutadapt:2.9--py37h516909a_0',
'debian': 'docker://debian:buster-slim',
'fastqc': 'docker://quay.io/biocontainers/fastqc:0.11.7--4',
......
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