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Merge pull request #404 from nf-core/cheaha_singularity_update

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Cheaha Config Update
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Lara Ianov 2022-08-30 14:45:50 -05:00 committed by GitHub
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6
conf/cheaha.config
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@ -5,9 +5,15 @@ params {
config_profile_url = 'https://www.uab.edu/cores/ircp/bds' config_profile_url = 'https://www.uab.edu/cores/ircp/bds'
} }
env {
TMPDIR="$USER_SCRATCH"
SINGULARITY_TMPDIR="$USER_SCRATCH"
}
singularity { singularity {
enabled = true enabled = true
autoMounts = true autoMounts = true
runOptions = "--contain --workdir $USER_SCRATCH"
} }
process { process {

2
docs/cheaha.md
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@ -13,6 +13,8 @@ module load Singularity
module load Nextflow module load Nextflow
``` ```
Various tasks will be run inside of Singularity containers and all temp files typically written to `/tmp` and `/var/tmp` are instead written to the path pointed to by the `USER_SCRATCH` environment variable. This means that these temp files are stored in a user specific location, making them inaccessible to other users for pipeline reruns. Some of these temp files can be large and cleanup is also the responsibility of the user.
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. 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 HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br> > NB: You will need an account to use the HPC cluster on Cheaha in order to run the pipeline. If in doubt contact UAB IT Research Computing.</br></br>