---
# System prepended metadata

title: 'Zurich ngff hackathon debrief: 2024-11-20'

---

Task:
---
Wrap an existing Fractal function into different `workflow managers`

1. Fractal
2. Snakemake
3. Nextflow
4. Dask


Snakemake:
---

Requirements:
1. Conda env with `fractal-task-core` package
2. Snakemake `yaml` config file with parameters

Rule syntax:
![snakemake_thres_rule](https://hackmd.io/_uploads/rk2yDYiz1e.png)

Execution:
![snakemake_thres](https://hackmd.io/_uploads/HyBwIYizJx.png)

Orig:
![orig_thresss](https://hackmd.io/_uploads/rJGB5Yjfyg.png)

Result:
![labeled_zarr](https://hackmd.io/_uploads/H1aKDFiGJe.png)
![thres000](https://hackmd.io/_uploads/rkdt5YjMyl.png)

```bash
snakemake --configfile ../configs/parameters.yaml
```









Nextflow version:
---
It runs `without modifying` the fractal task script. Additional steps that was required:
1. Container with `fractal-task-core` package:
2. Generate a on-disk version of the json file for argument parsing
3. a placeholder for the output config file, i.e. `out.json

nf-core compatible:

![Screenshot 2024-11-20 at 16.49.39](https://hackmd.io/_uploads/HJb7rtsfyl.png)


`
nf-core modules -g https://github.com/BioinfoTongLI/modules.git -b develop install fractal/thresholding
`