nbisweden/fega-sweden-helpdesk-generate-files

A Snakelike workflow to generate unique FASTQ files

Workflow for generating FASTQ files

Snakemake workflow to generate artificial files in FASTQ format for testing purposes. This workflow ensures that the files not only are given unique filenames, but also that the sequence identifiers within the files are unique (the generated files will thus have different checksums).

By providing a prefix to the filenames and sequence identifiers, you can ensure that files differ between runs. The workflow will use a timestamp as prefix by default. By default, the workflow will generate 4 files.

Prerequisites

• Python 3
• Snakemake

Usage

For running the workflow on a single core with default settings:

snakemake -c 1

Output files will be stored in a folder named output/.

To generate let say 20 files, you could enter the following command:

snakemake -c 1 --config numFiles=20

A timestamp will be prefixed to the resulting file names and sequence identifiers by default. If you wishm you can provide a custom prefix instead:

snakemake -c 1 --config prefix="submission1_" numFiles=20

Post processing

If you want to compress each file separately, you can run the following command inside the output/ folder:

find . -type f -execdir tar -zcvf '{}.tar.gz' '{}' \;