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https://github.com/hallerpatrick/nextflow-exercises
https://github.com/hallerpatrick/nextflow-exercises
Last synced: 10 days ago
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- Host: GitHub
- URL: https://github.com/hallerpatrick/nextflow-exercises
- Owner: HallerPatrick
- Created: 2021-05-21T13:28:53.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2021-07-01T18:23:41.000Z (over 3 years ago)
- Last Synced: 2024-12-08T18:04:56.541Z (17 days ago)
- Language: Nextflow
- Size: 304 MB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# nextflow-exercises
All exercises for the seminar Workflows for Scientific Data Analysis with Nextflow.
All workflow scripts are under the `workflow` directory, while the python scripts which are
actually doing the logic are under `lib`.
Results are written into `results`.
# Sample Project
## Overview
```mermaid
graph LR
A{ Source Texts } --> Tokenization --> Kmers & Frequncy --> E[Merge Results]
```
## Results of running nextflow pipelines
| Pipeline | URL | Deployability | Docker | Reason |
| --- | --- | --- | --- | --- |
| RNA-seq | https://github.com/nextflow-io/rnatoy | S | Ubuntu | - |
| RNA-seq | https://github.com/nextflow-io/rnaseq-nf | S | Debian | - |
| MTA-NF | https://github.com/cbcrg/mta-nf | F | Debian | Outdated links for downloading dependencies |
| AMPA-NF | https://github.com/cbcrg/ampa-nf | MiP | Debian | Missing Perl dependencies |
| cegwas2-nf | https://github.com/AndersenLab/cegwas2-nf | MaP | - | Conda environemnt needed, couldnt be set up |
| YAMP | https://github.com/alesssia/YAMP | MiP | - | Download of external database |
| FA-nf | https://github.com/anvlasova/FA-nf | MiP | - | Download external data |
| | | | | |
S: Success, instantly runnable
MiP: Minor Problems
MaP: Major Problems
F: Failure