bcl2fastq needs to be tested on hasta. ~It's important to note that the version of bcl2fastq on hasta and thalamus differ:~ The script demux-novaseq.bash actually uses /usr/local/bcl2fastq/bin/bcl2fastq, which version matches the version of bcl2fastq on hasta.
bcl2fastq -- version on hasta:
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.
/usr/local/bcl2fastq/bin/bcl2fastq --version on thalamus:
BCL to FASTQ file converter
bcl2fastq v2.20.0.422
Copyright (c) 2007-2017 Illumina, Inc.
bcl2fastq needs to be tested on hasta. ~It's important to note that the version of bcl2fastq on hasta and thalamus differ:~ The script
demux-novaseq.bash
actually uses/usr/local/bcl2fastq/bin/bcl2fastq
, which version matches the version of bcl2fastq on hasta.bcl2fastq -- version
on hasta:/usr/local/bcl2fastq/bin/bcl2fastq --version
on thalamus:Novaseq demultiplexing bcl2fastq command:
${BCL2FASTQ_BIN} = /usr/local/bcl2fastq/bin/bcl2fastq (declared in
demux-novaseq.bash
) ${IN_DIR} = input parameter ${OUT_DIR} = derived in script ${UNALIGNED_DIR} = derived in script ${BASEMASK} = derived in script usingdemux basemask create --application nova ${IN_DIR}
HiSeq2500 demultiplexing bcl2fastq command:
I can find no reason why we can't demux 2500 FCs with
bcl2fastq
so perhaps we should replaceconfigureBclToFastq.pl