.github/CONTRIBUTING.md

.github/markdownlint.yml

.gitignore

.travis.yml

CHANGELOG.md

CODE_OF_CONDUCT.md

README.md

assets/email_template.txt

assets/multiqc_config.yaml

assets/sendmail_template.txt

bin/scrape_software_versions.py

conf/awsbatch.config

conf/base.config

conf/igenomes.config

conf/test.config

docs/configuration/local.md

docs/configuration/reference_genomes.md

docs/installation.md

docs/output.md

docs/troubleshooting.md