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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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gzip -c filename.fastq > filename.fastq.gz |
3.b batchalternatively 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 |
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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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