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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-10-04 10:35:51 +1000 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2018-10-04 10:35:51 +1000 |
| commit | eb9364946e4b8e8a833d4b2ef9c975bbe01b8130 (patch) | |
| tree | 6d4962a994a3198c9571005090f16d75b257714a | |
| parent | 3aa8f5c3b9ea77fa6fc1186c0037549c09d6804d (diff) | |
Stuff to match & points of difference
| -rw-r--r-- | abcbs_2018.md | 27 |
1 files changed, 27 insertions, 0 deletions
diff --git a/abcbs_2018.md b/abcbs_2018.md index 37c4095..a8adc45 100644 --- a/abcbs_2018.md +++ b/abcbs_2018.md @@ -15,3 +15,30 @@ Justin Bedő, Leon Di Stefano, and Tony Papenfuss > We will demonstrate how Nix with our extensions can be used to succinctly specify a typical bioinformatics pipeline and contrast this against other dedicated bioinformatics pipeline languages. > We then show how it can be executed in whole or in part on an HPC queuing system > Finally, we show that the pipeline can also be executed using cloud resources. + +### Stuff to match in competitors + +- **A few standard pipelines** +- Dealing with big files +- Slightly complicated analyses +- local, HPC, and cloud execution +- Resumable, parallel +- Bioconda import + +### Points of difference + +- **Full-stack reproduciblity with one tool** +- **A language rather than a configuration format (cf. CWL/Javascript)** +- Not bioinformatics-specific +- Mature (~10y) +- Containers obsolete (but easy to generate) +- Higher level of reproducibility overall (hashing of inputs, outputs, derivations) +- Safety + - Declarative language + - Type/tag system (to do) + +### Weaknesses + +- Small bioinformatics collection +- No build execution stats +- Subtleties around filesystems and the Nix store |