Software

cutadapt (https://cutadapt.readthedocs.org/en/stable/)

Run

docker run -it --rm -v ${DATA_DIR}:/data emihat/cutadapt:latest cutadapt -f fastq -a ADAPTER_SEQ [-a ADAPTER_SEQ2 .. ] -o /data/${OUTPUT.fastq} /data/${INPUT.fastq}

Dockerfile

FROM python
MAINTAINER emihat <hattori.emi@imsbio.co.jp>
RUN pip install cutadapt
CMD /usr/local/bin/cutadapt