bcl2fastq
Link to section 'Introduction' of 'bcl2fastq' Introduction
bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
Docker hub: https://hub.docker.com/r/gcfntnu/bcl2fastq
Home page: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Link to section 'Versions' of 'bcl2fastq' Versions
- 2.20.0
Link to section 'Commands' of 'bcl2fastq' Commands
- bcl2fastq
Link to section 'Module' of 'bcl2fastq' Module
You can load the modules by:
module load biocontainers
module load bcl2fastq
Link to section 'Example job' of 'bcl2fastq' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run bcl2fastq on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=bcl2fastq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers bcl2fastq