README

# Sisyphus-style checksums

This pipeline takes a runfolder and an include file and generates a checksum
file compatible with [Sisyphus](https://github.com/Molmed/sisyphus).

## Usage

```nextflow
nextflow run main.nf --input_folder <path_to_runfolder> --include_file <path_to_include_file> [--ignore_cache]
```

### Running on Uppmax
When running on Uppmax, use `-profile uppmax` and specify project with `--project <uppmax project>`

## Input
- `--input_folder <path_to_runfolder`: path to the runfolder for which the
checksums need to be generated
- `--include_file <path_to_include_file`: determines which files should appear
in the checksums (same format as `rsync`)
- `--ignore-cache` whether or not to use previously computed checksums. When
this flag is set, the pipeline will ignore previously computed checksum.
Otherwise, it will keep the checksums available in `MD5/checksums.md5` in the
input runfolder.

## Output

The pipeline will write the results at `MD5/checksums.md5` in the input runfolder.

## Running the tests
```
nf-test test
```