path: root/references.bib

@article{platypus,
  doi = {10.1038/ng.3036},
  url = {https://doi.org/10.1038/ng.3036},
  year  = {2014},
  month = jul,
  publisher = {Springer Nature},
  volume = {46},
  number = {8},
  pages = {912--918},
  author = {Andy Rimmer and Hang Phan and Iain Mathieson and Zamin Iqbal and Stephen R F Twigg and Andrew O M Wilkie and Gil McVean and Gerton Lunter},
  title = {Integrating mapping-,  assembly- and haplotype-based approaches for calling variants in clinical sequencing applications},
  journal = {Nature Genetics}
}
@online{vieira_truly_2017,
  title = {A truly reproducible scientific paper?},
  url = {https://medium.com/@bmpvieira/a-truly-reproducible-scientific-paper-5059b282ee9a},
  abstract = {The current situation},
  titleaddon = {Bruno Vieira},
  author = {Vieira, Bruno},
  urldate = {2019-01-23},
  date = {2017-02-01}
}

@online{archibald_reproducible_2017,
  title = {Reproducible Environments With Nix},
  url = {https://www.software.ac.uk/blog/2017-10-05-reproducible-environments-nix},
  titleaddon = {Software Sustainability Institute},
  author = {Archibald, Blair},
  urldate = {2019-01-23},
  date = {2017-10-05}
}

@article{crouch_software_2013,
  title = {The Software Sustainability Institute: Changing Research Software Attitudes and Practices},
  volume = {15},
  issn = {1521-9615},
  doi = {10.1109/MCSE.2013.133},
  shorttitle = {The Software Sustainability Institute},
  abstract = {To effect change, the Software Sustainability Institute works with researchers, developers, funders, and infrastructure providers to identify and address key issues with research software.},
  pages = {74--80},
  number = {6},
  journaltitle = {Computing in Science Engineering},
  author = {Crouch, S. and Hong, N. C. and Hettrick, S. and Jackson, M. and Pawlik, A. and Sufi, S. and Carr, L. and Roure, D. De and Goble, C. and Parsons, M.},
  date = {2013-11},
  keywords = {domain engineering, Domain engineering, maintainability, Programming, reliability, research and development, research software attitudes, research software practices, scientific computing, Scientific computing, Software development, software engineering, Software engineering, Software reliability, Software Sustainability Institute, Training}
}

@misc{georges_dubus_mix:_2018,
  location = {London},
  title = {Mix: Nix for data pipeline configuration},
  url = {https://www.youtube.com/watch?v=tc5ApNqhAQ4},
  howpublished = {NixCon},
  year = {2018},
  author = {{Georges Dubus}},
}

@online{noauthor_wdl_nodate,
  title = {{WDL} {\textbar} Home},
  url = {https://software.broadinstitute.org/wdl/},
  urldate = {2019-01-23}
}

@online{noauthor_reusable_2019,
  title = {Reusable Reproducible Composable Software},
  rights = {{MPL}-2.0},
  url = {https://github.com/fractalide/fractalide},
  publisher = {Fractalide},
  date = {2019-01-22},
}
@article{gruning_practical_2018,
  title = {Practical Computational Reproducibility in the Life Sciences},
  volume = {6},
  issn = {2405-4712},
  url = {https://www.cell.com/cell-systems/abstract/S2405-4712(18)30140-6},
  doi = {10.1016/j.cels.2018.03.014},
  pages = {631--635},
  number = {6},
  journaltitle = {Cell Systems},
  shortjournal = {cels},
  author = {Grüning, Björn and Chilton, John and Köster, Johannes and Dale, Ryan and Soranzo, Nicola and Beek, Marius van den and Goecks, Jeremy and Backofen, Rolf and Nekrutenko, Anton and Taylor, James},
  urldate = {2018-11-20},
  date = {2018-06-27},
  pmid = {29953862}
}
@online{noauthor_haskell_2019,
  title = {A Haskell re-implementation of the Nix expression language},
  url = {https://github.com/haskell-nix/hnix},
  publisher = {Nix in Haskell},
  date = {2019-01-22}
}

@misc{amstutz_common_2016,
  title = {Common Workflow Language, v1.0},
  url = {https://figshare.com/articles/Common_Workflow_Language_draft_3/3115156},
  abstract = {The Common Workflow Language ({CWL}) is an informal, multi-vendor working group consisting of various organizations and individuals that have an interest in portability of data analysis workflows.  Our goal is to create specifications that enable data scientists to describe analysis tools and workflows that are
powerful, easy to use, portable, and support reproducibility.{CWL} builds on technologies such as {JSON}-{LD} and Avro for data modeling and Docker for portable runtime environments.

{CWL} is designed to express workflows for data-intensive science, such as Bioinformatics, Medical Imaging, Chemistry, Physics, and Astronomy.This is v1.0 of the {CWL} tool and workflow specification, released on 2016-07-08.The specification, in {HTML} format, is in the draft-3/docs folder.},
  author = {Amstutz, Peter and Crusoe, Michael R. and Tijanić, Nebojša and Chapman, Brad and Chilton, John and Heuer, Michael and Kartashov, Andrey and Leehr, Dan and Ménager, Hervé and Nedeljkovich, Maya and Scales, Matt and Soiland-Reyes, Stian and Stojanovic, Luka},
  urldate = {2019-01-23},
  date = {2016-07-08},
  doi = {10.6084/m9.figshare.3115156.v2},
  keywords = {commonwl}
}
@article{cnvkit,
  doi = {10.1371/journal.pcbi.1004873},
  url = {https://doi.org/10.1371/journal.pcbi.1004873},
  year  = {2016},
  month = apr,
  publisher = {Public Library of Science ({PLoS})},
  volume = {12},
  number = {4},
  pages = {e1004873},
  author = {Eric Talevich and A. Hunter Shain and Thomas Botton and Boris C. Bastian},
  title = {{CNVkit}: Genome-Wide Copy Number Detection and Visualization from Targeted {DNA} Sequencing},
  journal = {{PLOS} Computational Biology}
}
@article{di_tommaso_nextflow_2017,
  title = {Nextflow enables reproducible computational workflows},
  volume = {35},
  rights = {2017 Nature Publishing Group},
  issn = {1546-1696},
  url = {https://www.nature.com/articles/nbt.3820},
  doi = {10.1038/nbt.3820},
  abstract = {Nextflow enables reproducible computational workflows},
  pages = {316--319},
  journaltitle = {Nature Biotechnology},
  author = {Di Tommaso, Paolo and Chatzou, Maria and Floden, Evan W. and Barja, Pablo Prieto and Palumbo, Emilio and Notredame, Cedric},
  urldate = {2019-01-23},
  date = {2017-04-11},
  langid = {english}
}
@article{strelka,
  doi = {10.1038/s41592-018-0051-x},
  url = {https://doi.org/10.1038/s41592-018-0051-x},
  year  = {2018},
  month = jul,
  publisher = {Springer Nature America,  Inc},
  volume = {15},
  number = {8},
  pages = {591--594},
  author = {Sangtae Kim and Konrad Scheffler and Aaron L. Halpern and Mitchell A. Bekritsky and Eunho Noh and Morten K\"{a}llberg and Xiaoyu Chen and Yeonbin Kim and Doruk Beyter and Peter Krusche and Christopher T. Saunders},
  title = {Strelka2: fast and accurate calling of germline and somatic variants},
  journal = {Nature Methods}
}
@article{samtools,
  doi = {10.1093/bioinformatics/btp352},
  url = {https://doi.org/10.1093/bioinformatics/btp352},
  year  = {2009},
  month = jun,
  publisher = {Oxford University Press ({OUP})},
  volume = {25},
  number = {16},
  pages = {2078--2079},
  author = {H. Li and B. Handsaker and A. Wysoker and T. Fennell and J. Ruan and N. Homer and G. Marth and G. Abecasis and R. Durbin and},
  title = {The Sequence Alignment/Map format and {SAMtools}},
  journal = {Bioinformatics}
}
@article{bwa,
  doi = {10.1093/bioinformatics/btp324},
  url = {https://doi.org/10.1093/bioinformatics/btp324},
  year  = {2009},
  month = may,
  publisher = {Oxford University Press ({OUP})},
  volume = {25},
  number = {14},
  pages = {1754--1760},
  author = {H. Li and R. Durbin},
  title = {Fast and accurate short read alignment with Burrows-Wheeler transform},
  journal = {Bioinformatics}
}
@online{bwa-mem,
Author = {Heng Li},
Title = {Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM},
Year = {2013},
eprinttype = {arXiv},
eprint = {q-bio/1303.3997},
}
@article{Bed2019,
  doi = {10.7717/peerj.7223},
  url = {https://doi.org/10.7717/peerj.7223},
  year = {2019},
  month = jul,
  publisher = {{PeerJ}},
  volume = {7},
  pages = {e7223},
  author = {Justin Bed{\H{o}}},
  title = {{BioShake}: a Haskell {EDSL} for bioinformatics workflows},
  journal = {{PeerJ}}
}
@online{bioshake-git,
  title = {Bioshake},
  url = {https://github.com/PapenfussLab/bioshake},
  month = jan,
  year = {2019}
}

@online{torque,
title={TORQUE Resource Manager},
month = jan,
year = {2019},
url = {http://www.adaptivecomputing.com/products/torque/}
}
@online{wdl-scatter-gather,
title={Workflow Description Language - Specification and Implementations},
month = jan,
year = {2019},
url = {https://github.com/openwdl/wdl/blob/721e16f28f0bf5b3ae8b44df2859b504e10ae13f/README.md#scattergather}
}
@online{nextflow-example,
title = {Nextflow - Basic pipeline},
month = jan,
year = {2019},
url = {https://www.nextflow.io/example1.html}
}
@online{docker,
title = {Enterprise container platform},
month = oct,
year = {2018},
url = {https://www.docker.com}
}
@online{singularity,
  title = {Singularity},
  month = oct,
  year =