Prepared by the eResearch Office, QUT.
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#load python 3.7 module load phyton3.7python/3.9.6-gcccore-11.2.0 #download script and make executable wget -L https://raw.githubusercontent.com/nf-core/rnaseq/master/bin/fastq_dir_to_samplesheet.py chmod +x fastq_dir_to_samplesheet.py #generate the samplesheet.csv file fastq_dir_to_samplesheet.py /path/to/directory/containing/fastq_files/ samplesheet.csv \ --strandedness unstranded \ --read1_extension R1.fastq.gz \ --read2_extension R2.fastq.gz |
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#delete the existing assests associated with the RNAseq pipeline: cd ~/.nextflow/assets/nf-core rm -r rnaseq/ #run again a test with the new version that you are testing, for example, version 3.10.1. See details on how to run a test above (under 'Getting Started') |
Add output folders/files
sample data
Running the pipeline using custom data
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