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

How to use

1. Install Nextflow https://www.nextflow.io/docs/latest/getstarted.html#installation

2. 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.