Collection of tools to help users upload, process and download FASTQ files for GPAS. This is a quick repository intended to help the users taking part in the GPAS pilot and is not yet production code. At present it is limited to

• Illumina paired FASTQs
• Mycobacterial samples

For example, consider having a folder data/ containing 10 pairs of illumina FASTQ files named sample01_1.fastq.gz, sample01_2.fastq.gz... sample10_1.fastq.gz, sample10_2.fastq.gz.

If I want to composite a basic upload CSV file where the samples where all collected in England on 10 Jan 2024 I would issue

$ python gpas-create-uploadcsv.py --input-dir data/ --collection-date 2024-01-10 --country GBR

Note that the date has to be in ISO-8601 format and the country has to be a valid ISO-3166 3-letter code, here GBR. This will then produce a single file upload.csv specifying all ten samples. One can then edit this file to e.g. modify some of the collection dates or make some of the samples positive or negative controls.

On the other hand, if I want to upload these ten samples as two batches, I can issue

$ python gpas-create-uploadcsv.py --input-dir data/ --collection-date 2024-01-10 --country GBR --number-of-batches 2

And two files, upload-0.csv and upload-1.csv, will be created each with five samples. This can be useful if e.g. your network connection occasionally drops.