prepare-nf

Generate a run sample sheet to input to amplicon-nf.

This workflow is primarily designed to be run via a GUI such as EPI2ME and a general guide can be found here.

If you want to run on the command line

Required arguments are:

• run_dir - the directory where reads have been generated by the sequencer e.g. for ONT this will be a directory containing a subdirectory of fastq for each barcode
• platform - currently only supports "ont"/"nanopore"
• metadata - a CSV or XLS file containing barcode and sample columns, often called a "sample sheet"
• amplicon_scheme - either a primal-scheme name in the format <name>/<length>/<version> or a custom scheme name (in which case --custom_scheme_path must also provided)

Example command:

nextflow run artic-network/prepare-nf --platform ont --run_dir test --metadata test/samplesheet.csv --amplicon_scheme custom/3000/v1.0.0

This pipeline will then generate a sample_config.csv file which can be input directly to amplicon-nf. This CSV file populates all sample rows with the shared metadata about platform and amplicon scheme, and a fastq path for each barcode found in the run directory. It will exclude any sample/barcode rows where there is no sample name provided, or no where no fastq files were found for the specified barcode.