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The nf-core/bactmap workflow requires Nextflow to be installed in your account on the HPC. Find details on how to install and test Nextflow here prepare a nextflow.config file and run a PBS pro submission script for Nextflow pipelines.
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singularity run docker://ncbi/sra-tools:latest fastq-dump -X 1000000 -I --split-files SRR1198667 |
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3.a compress the fastq files
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gzip -c filename.fastq > filename.fastq.gz |
3.b alternatively run a loop to compress all fastq files in the folder:
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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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When specifying the path to the data files, it is more portable to use absolute paths rather than relative paths.
check if ascii characters were added in your samplesheet.csv file:
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cat -A samplesheet.csv |
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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