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singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667 |
Pipeline summary
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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When specifying the path to the data files, it is more portable to use absolute paths rather than relative paths.
Creating the samplesheet.csv file using Excel can add ascii characters, run the following command to remove them:
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dos2unix samplesheet.csv |
Preparing to run on the HPC
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