This pipeline was developed to download data from SRA and process it in parallel. The meta file and all of the data assume that you are wanting to download the data for process. If you want to use your own data, you will need to manipulate the meta file and directory structure so that you skip fasterq-dump and proceed to read trimming.
The meta file is a .tsv file that has at least three columns named condition, srx, srr. The biological replicate is considered the srx ID and the technical replicate is considered the srr ID. If you have more than one srr ID per srx ID the technical replicates will be merged into a single srx based output. The code will use the srr ID to download the .fastq files that are to be processed. Right now you must provide all the srr ID values for a srx ID on your own.
A third column is available called condition that can be used to create a condition grouping for the samples. The example below will create directories and information using the condition as the final name.
Example meta file:
condition srr srx
GM12878 SRR5427886 SRX2717911
GM12878 SRR5427887 SRX2717912