Commit b585ff80 authored by van den Berg's avatar van den Berg
Browse files

Speed up cutadapt

Use 8 cores instead of just 1, according to the documentation speed
should almost scale linear with the cores provided.

Also reduce the compression level on the output file, since most time
for cutadapt is spent re-compressing the data after trimming the
adapters.
parent 1d79ec4c
......@@ -160,6 +160,7 @@ rule cutadapt:
container: containers["cutadapt"]
shell: "cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG "
"--minimum-length 1 --quality-cutoff=20,20 "
"--compression-level=1 -j 8 "
"--output {output.r1} --paired-output {output.r2} -Z "
"{input.r1} {input.r2} "
"--report=minimal > {log}"
......
......@@ -19,6 +19,7 @@ covstats:
vmem: 6G
cutadapt:
threads: 8
time: 0-2
fastqc_raw:
......
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