This is the repository for the nextflow pipeline to preprocess GridION fastq files and preparing a samplesheet.csv for nf-core/nanoseq DNA protocol.

The pipeline is will take an in-house parquet file with metadata (sample, replicate, barcode, and more) and together with a experiement project directory a compatible samplesheet.csv will be generated.

Expected input prarams:

*parquetpath - path tp parquet file of metadata

• publishDir - location to put samplesheet.csv - merged fastq files will be in a subdirectory called fastq_merged

*fasta - path to reference fasta file

*gtf - path to reference fasta file

• reference - to be implemented: string which is the ID of strain, used to define URL to fasta and gtf