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singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667 |
compress the fastq files
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gzip -c filename.fastq > filename.fastq.gz |
batch:
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for file in `ls *.fastq`; do echo $file; gzip -c $file > ${file}.gz; done |
Getting Started
Download and run the workflow using a minimal data provided by nf-core/bactmap. We recommend using singularity as the profile for QUT’s HPC. Note: the profile option ‘docker’ is not available on the HPC.
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