biotech
Overview
main.bash -- contains pipeline implemented as bash script
./toil-hello-worlds -- contains useful toil examples
toil-pipeline.py -- pipeline implemented with toil
Usage
Downloads resources:
- https://www.ncbi.nlm.nih.gov/sra/SRX18175272 as sequence.fastq.gz
- https://www.ncbi.nlm.nih.gov/assembly/GCF_000005845.2/ as reference.fna
It is expected that you have bwa, fastqc, samtools on your PATH
For toil pipeline it is expected that input folder contains reference.fna and sequence.fastq.gz
python toil-pipeline.py file:my-job-store --logFile="./log.txt"
main.bash reference.fna.gz sequence.fastq.gz
Logs
See ./log.txt for example of a log when mapping is > 90%
See ./res-log.txt for example of a log when mapping is < 90%