mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-22 08:29:54 +00:00
Create cambridge.md
This commit is contained in:
parent
8b3951b244
commit
29dcc160e3
1 changed files with 17 additions and 0 deletions
17
docs/cambridge.md
Normal file
17
docs/cambridge.md
Normal file
|
@ -0,0 +1,17 @@
|
||||||
|
# nf-core/configs: Cambridge HPC Configuration
|
||||||
|
All nf-core pipelines have been successfully configured for use on the Cambridge HPC cluster at the [The University of Cambridge](https://www.cam.ac.uk/).
|
||||||
|
To use, run the pipeline with `-profile cambridge`. This will download and launch the [`cambridge.config`](../conf/cambridge.config) whichhas been pre-configured
|
||||||
|
with a setup suitable for the Cambridge HPC cluster. Using this profile, either a docker image containing all of the required software will be downloaded,
|
||||||
|
and converted to a Singularity image or a Singularity image downloaded directly before execution of the pipeline.
|
||||||
|
|
||||||
|
The latest version of Nextflow is not installed by default on the Cambridge HPC cluster. You will need to install it into a directory you have write access to.
|
||||||
|
Follow these instructions from the Nextflow documentation.
|
||||||
|
|
||||||
|
- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
|
||||||
|
|
||||||
|
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline
|
||||||
|
has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
|
||||||
|
|
||||||
|
> NB: You will need an account to use the Cambridge HPC cluster in order to run the pipeline. If in doubt contact IT.
|
||||||
|
> NB: Nextflow will need to submit the jobs via SLURM to the Cambridge HPC cluster and as such the commands above will have to be executed on one of the login
|
||||||
|
nodes. If in doubt contact IT.
|
Loading…
Reference in a new issue