The file environment_requirements.txt contains all the packages in the conda enviorment used to create the pipeline and run it. Not all packages in the file are probably needed, but also not all of the needed tools are in the file. Therefore the tools list down below contains just the tools needed by the pipeline and packages called in scripts.
- samtools
- picard
- GATK3.8
- trimmomatic
- fastp
- python3.8
- FastQC
- BWA
- sqlite3
- pandas
- numpy