mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 08:29:54 +00:00
16 lines
1.2 KiB
Markdown
16 lines
1.2 KiB
Markdown
# nf-core/configs: Hasta Configuration
|
|
|
|
## Using the Hasta config profile
|
|
|
|
Before running the pipeline `Nextflow` will need to be install in the conda environment being used.
|
|
|
|
To use, run the pipeline with `-profile hasta` (one hyphen).
|
|
This will download and launch the [`hasta.config`](../conf/hasta.config) which has been pre-configured with a setup suitable for the hasta servers.
|
|
It will enable `Nextflow` to manage the pipeline jobs via the `Slurm` job scheduler.
|
|
Using this profile, `Docker` image(s) containing required software(s) will be downloaded, and converted to `Singularity` image(s) if needed before execution of the pipeline.
|
|
|
|
Recent version of `Nextflow` also support the environment variable `NXF_SINGULARITY_CACHEDIR` which can be used to supply images. A use case: `NXF_SINGULARITY_CACHEDIR=/path/to/images; export NXF_SINGULARITY_CACHEDIR` before running the pipeline.
|
|
|
|
## Development and production config
|
|
|
|
Each user on hasta has a priority based on their allocated team, either development or production. To enable this when submitting a job to Slurm, submit with `-profile hasta,dev_prio` or `-profile hasta,prod_prio`. This overwrites certain parts of the config and submits the job based on different priorities.
|