millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-22 16:29:55 +00:00
Code Issues Releases Packages Activity

Pipeline specific configs moving to confs/pipeline

Browse source
This commit is contained in:
ameynert 2021-03-23 16:07:07 +00:00 committed by GitHub
parent b48136a62e
commit 791f3c95f3
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 0 additions and 8 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

8
docs/eddie.md
View file

@ -33,14 +33,6 @@ module load igmm/apps/nextflow
This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity for software management. This config enables Nextflow to manage the pipeline jobs via the SGE job scheduler and using Singularity for software management.
### Pipeline-specific config files
In addition to the generic nf-core configuration accessed via `-profile eddie`, there are pipeline-specific configuration files in the NextGenResources fileset to handle processes that are known to require specific custom configuration on the eddie system, in particular Java processes which require an extra memory overhead. For example:
```bash
nextflow run nf-core/rnaseq -profile eddie -c /exports/igmm/eddie/NextGenResources/nextflow/conf/eddie.rnaseq.config # ...rest of pipeline flags
```
## Singularity set-up ## Singularity set-up
Load Singularity from the module system and set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline. Load Singularity from the module system and set the Singularity cache directory to the NextGenResources path for the pipeline and version you want to run. If this does not exist, please contact the [IGMM Data Manager](data.manager@igmm.ed.ac.uk) to have it added. You can add these lines to the file `$HOME/.bashrc`, or you can run these commands before you run an nf-core pipeline.