Demutliplex a MiSEQ or NextSEQ run, perform QC using FastQC and MultiQC and deliver files either to VIGASP for analysis or NIRD for archiving
Replace
Note: don't bother with enforcing ISO dates for the directory name. It is an Illumina standard and they do not care.
Software requirements
Python > v3.9
bcl2fastq ( from https://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html )
FastQC ( https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ )
MultiQC ( pip3 install multiqc )
├── bin binaries and symlinks of binaries live here
├── clarity exported Illumina Clarity directory
│ ├── gls_events
│ ├── logs clarity logs go here
│ ├── miseq miseq-clarity stopover directory
│ │ └── M06578 per serial number
│ │ └── samplesheets samplesheets for this serial number gohere
│ └── nextseq nextseq-clarity stopover directory
│ └── NB552450 per serial number
│ └── samplesheets samplesheets for this serial number gohere
├── demultiplex demultiplexed data directory
├── for_transfer data ready to be transfered over to NIRD or VIGASP
├── logs all demultiplexing logs go here
├── rawdata raw data directory, sequencers write here
│ ├── bad_runs runs which are bad, or rejected
│ └── control_runs water/other control runs
└── samplesheets cummulative backups of all samplesheets
├── M06578 -> /data/clarity/miseq/M06578/samplesheets/ symlinmk to sample sheets for convinience
└── NB552450 -> /data/clarity/nextseq/NB552450/samplesheets/ symlinmk to sample sheets for convinience
Example:
Z:\190912_M06578_0001_000000000-CNNTP
├── SampleSheets.csv
Z:\SampleSheets
├── 190912_M06578_0001_000000000-CNNTP.csv
/usr/bin/python3 /data/bin/demultiplex_script.py \<RunID\>
as the relevant user.