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Commit 109f45bc authored by van den Berg's avatar van den Berg
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Merge branch 'master' into 'known-snps'

# Conflicts:
#   Snakefile
parents 90d19440 ac9d88c6
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1 merge request!13Deprecate conda, make pipeline more general
Pipeline #3109 failed
......@@ -522,7 +522,7 @@ rule fastqc_raw:
output:
aux="{sample}/pre_process/raw_fastqc/.done.txt"
singularity: "docker://quay.io/biocontainers/fastqc:0.11.7--4"
shell: "fastqc --nogroup -o {params.odir} {input.r1} {input.r2} "
shell: "fastqc --threads 4 --nogroup -o {params.odir} {input.r1} {input.r2} "
"&& echo 'done' > {output.aux}"
......
......@@ -7,7 +7,7 @@ align:
threads: 8
vmem: 4G
markdup:
vmem: 10G
vmem: 20G
baserecal:
threads: 8
vmem: 6G
......@@ -24,6 +24,12 @@ genotype_gather:
covstats:
vmem: 6G
multiqc:
vmem: 20G
vmem: 30G
split_vcf:
vmem: 20G
fastqc_raw:
threads: 4
fastqc_merged:
threads: 4
fastqc_postqc:
threads: 4
......@@ -23,7 +23,7 @@ output_r1=${3}
output_r2=${4}
odir=${5}
fastqc --nogroup -o ${odir} ${input_r1} ${input_r2}
fastqc --threads 4 --nogroup -o ${odir} ${input_r1} ${input_r2}
if [[ -f ${output_r1} ]]; then
unzip -l ${output_r1} || head -c 0 ${output_r1} > ${output_r1}
......
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