bowhan/bcl2fastq repository overview

i=XXXX
docker run --memory=10G --cpus=4 \
    -v /path/to/basemount/:/raw \
    -v /path/to/local/output:/out \
    bowhan/bcl2fastq:v2.20.0 \
    -r 1 \
    -p 2 \
    -w 1 \
    --barcode-mismatches 0 \
    --ignore-missing-bcls \
    --ignore-missing-filter \
    --ignore-missing-positions \
    --ignore-missing-controls \
    --auto-set-to-zero-barcode-mismatches \
    --find-adapters-with-sliding-window \
    --adapter-stringency 0.9 \
    --mask-short-adapter-reads 35 \
    --minimum-trimmed-read-length 35 \
    --no-lane-splitting  \
    --runfolder-dir /raw/$i/ \
    --sample-sheet /raw/$i/SampleSheet.csv \
    --output-dir /out/$i