millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-21 16:16:04 +00:00
Code Issues Releases Packages Activity

Merge pull request #377 from nvnieuwk/vsc_ugent

Browse source 
Typo in VSC UGent markdown
This commit is contained in:
Phil Ewels 2022-05-20 10:55:39 +02:00 committed by GitHub
commit 123706519e
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
1 changed files with 0 additions and 2 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
docs/vsc_ugent.md
View file

@ -19,8 +19,6 @@ module load Nextflow
nextflow run <pipeline> -profile vsc_ugent,<CLUSTER> <Add your other parameters>
```
I also highly recommend specifying a location of a Singularity cache directory, by specifying the location with the `$SINGULARITY_CACHEDIR` bash environment variable in your `.bash_profile` or `.bashrc` or by adding it to your PBS script. If this cache directory is not specified,
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.
The config contains a `cleanup` command that removes the `work/` directory automatically once the pipeline has completed successfully. If the run does not complete successfully then the `work/` dir should be removed manually to save storage space. The default work directory is set to `$VSC_SCRATCH_VO_USER/work` per this configuration