@misc{pip,
title = {pip},
url = {https://pip.pypa.io/en/stable/}
}
@misc{bioconda,
title = {bioconda},
url = {https://bioconda.github.io/}
}
@article{Koster2012a,
abstract = {SUMMARY Snakemake is a workflow engine that provides a readable Python-based workflow definition language and a powerful execution environment that scales from single-core workstations to compute clusters without modifying the workflow. It is the first system to support the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. AVAILABILITY http://snakemake.googlecode.com. CONTACT johannes.koester@uni-due.de.},
author = {Koster, J. and Rahmann, S.},
doi = {10.1093/bioinformatics/bts480},
issn = {1367-4803},
journal = {Bioinformatics},
month = {oct},
number = {19},
pages = {2520--2522},
pmid = {22908215},
title = {{Snakemake--a scalable bioinformatics workflow engine}},
url = {http://www.ncbi.nlm.nih.gov/pubmed/22908215 https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts480},
volume = {28},
year = {2012}
}
@article{Vivian2017,
author = {Vivian, John and Rao, Arjun Arkal and Nothaft, Frank Austin and Ketchum, Christopher and Armstrong, Joel and Novak, Adam and Pfeil, Jacob and Narkizian, Jake and Deran, Alden D and Musselman-Brown, Audrey and Schmidt, Hannes and Amstutz, Peter and Craft, Brian and Goldman, Mary and Rosenbloom, Kate and Cline, Melissa and O'Connor, Brian and Hanna, Megan and Birger, Chet and Kent, W James and Patterson, David A and Joseph, Anthony D and Zhu, Jingchun and Zaranek, Sasha and Getz, Gad and Haussler, David and Paten, Benedict},
doi = {10.1038/nbt.3772},
issn = {1546-1696},
journal = {Nature biotechnology},
month = {apr},
number = {4},
pages = {314--316},
pmid = {28398314},
title = {{Toil enables reproducible, open source, big biomedical data analyses.}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3772 http://www.ncbi.nlm.nih.gov/pubmed/28398314},
volume = {35},
year = {2017}
}
@article{DiTommaso2017,
author = {{Di Tommaso}, Paolo and Chatzou, Maria and Floden, Evan W and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
doi = {10.1038/nbt.3820},
issn = {1546-1696},
journal = {Nature biotechnology},
month = {apr},
number = {4},
pages = {316--319},
pmid = {28398311},
title = {{Nextflow enables reproducible computational workflows.}},
url = {http://www.nature.com/doifinder/10.1038/nbt.3820 http://www.ncbi.nlm.nih.gov/pubmed/28398311},
volume = {35},
year = {2017}
}
