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#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 reverseunstranded \
--read1_extension R1.fastq.gz \
--read2_extension R2.fastq.gz |
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