jasmine-amir / microrunqc-wdl-JA

forked 2023 01 04

microrunqc-wdl Pipeline

Directories

• backends/ : Backend configuration files (.conf)
• workflow_opts/ : Workflow option files (.json)
• examples/ : input JSON examples (SE and PE)
• data/ : data TSV files for each platform
• src/ : scripts for each task in WDL
• docker/ : Dockerfiles
• test/ : test scripts for developers

A test input file

Use the paired-end data from here:

https://galaxytrakr.org/u/jpayne/h/big-olaf

{
    "paired_reads":[
        {"left":"SRR20708232/forward.fastqsanger.gz", "right":"SRR20708232/reverse.fastqsanger.gz"},
        {"left":"SRR20708233/forward.fastqsanger.gz", "right":"SRR20708233/reverse.fastqsanger.gz"},
        {"left":"SRR20708234/forward.fastqsanger.gz", "right":"SRR20708234/reverse.fastqsanger.gz"},
        {"left":"SRR20708235/forward.fastqsanger.gz", "right":"SRR20708235/reverse.fastqsanger.gz"},
        {"left":"SRR20708236/forward.fastqsanger.gz", "right":"SRR20708236/reverse.fastqsanger.gz"},
        {"left":"SRR20708237/forward.fastqsanger.gz", "right":"SRR20708237/reverse.fastqsanger.gz"}
    ]
}