Test bcl2fastq on Hasta

[barrystokman]

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.

Novaseq demultiplexing bcl2fastq command:

${BCL2FASTQ_BIN} --loading-threads 3 --processing-threads 15 --writing-threads 3 --runfolder-dir ${IN_DIR} --output-dir ${OUT_DIR}/${UNALIGNED_DIR} --use-bases-mask ${BASEMASK} --sample-sheet ${IN_DIR}/SampleSheet.csv --barcode-mismatches 1

${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 using demux basemask create --application nova ${IN_DIR}

HiSeq2500 demultiplexing bcl2fastq command:

/usr/local/bin/configureBclToFastq.pl --force --sample-sheet ${BASE}/Data/Intensities/BaseCalls/SampleSheet.csv --ignore-missing-bcl --ignore-missing-stats --use-bases-mask ${BASEMASK} --fastq-cluster-count 0 --input-dir ${BASE}/Data/Intensities/BaseCalls --output-dir ${DEMUX_DIR}/${RUN}/${UNALDIR} 2>&1 | sed -r "s/\x1B\[([0-9]{1,2}(;[0-9]{1,2})?)?[m|K]//g" >> ${PROJECTLOG}

I can find no reason why we can't demux 2500 FCs with bcl2fastq so perhaps we should replace configureBclToFastq.pl

[henrikstranneheim]

/usr/local/bcl2fastq/bin/bcl2fastq works. However, we are now using singularity containers instead