Sra-download

This pipeline downloads SRA files from NCBI and removes adapter sequences from paired end data using seqpurge.

How to use

Install Nextflow https://www.nextflow.io/docs/latest/getstarted.html#installation
Run the pipeline with the following command below, it will use pbelmann/sra-download docker container.

nextflow run  pbelmann/sra-download  --cache /path/to/cache --output /path/to/output --input /path/to/input.txt -with-trace -with-timeline -with-docker pbelmann/sra-download

where:

'/path/to/cache' is a directory for storing the downloaded .sra files
'/path/to/output' is a directory for storing the output data
'/path/to/input.txt' is a file downloaded from SRA Run Selector The column containing the SRA ids should have the name 'Run_s'

NOTE!:

You can use this pipeline without docker but then you will have to change the path to the sra toolkit and seqpurge in your config.
You can distribute the pipeline on a grid system by providing the executor in your config.