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- mkdir -p {params.outdir}
- /lustre1/ctgb-usr/local/src/bbmap/bbduk.sh \
- -Xmx14g \
- in={input.R1} in2={input.R2} \
- out={output.R1} out2={output.R2} \
- ref=/lustre1/genomes/Illumina_Adapters/BBDUK/adapters.fa \
- k=23 mink=11 rcomp=t ktrim=f kmask=X qtrim=rl trimq=5 \
- forcetrimleft=2 forcetrimright2=2 overwrite=true
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