parallel-fastq-dump
Link to section 'Introduction' of 'parallel-fastq-dump' Introduction
Parallel-fastq-dump
is the parallel fastq-dump wrapper.
For more information, please check its website: https://biocontainers.pro/tools/parallel-fastq-dump and its home page on Github.
Link to section 'Versions' of 'parallel-fastq-dump' Versions
- 0.6.7
Link to section 'Commands' of 'parallel-fastq-dump' Commands
- parallel-fastq-dump
Link to section 'Module' of 'parallel-fastq-dump' Module
You can load the modules by:
module load biocontainers
module load parallel-fastq-dump
Link to section 'Example job' of 'parallel-fastq-dump' 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 Parallel-fastq-dump on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=parallel-fastq-dump
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers parallel-fastq-dump
parallel-fastq-dump -s SRR11941281/SRR11941281.sra \
--split-files --threads 4 --gzip