feat(sysbio): Add cleanup

jingydz · Jun 17, 2021 · 41ae99d · 41ae99d
1 parent 87c8e34
commit 41ae99d
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diff --git a/conf/utd_sysbio.config b/conf/utd_sysbio.config
@@ -23,6 +23,9 @@ process {
   queue = { task.memory >= 30.GB && task.cpu <= 16 ? 'normal': 'smallmem' }
 }
 
+// Preform work directory cleanup after a successful run
+cleanup = true
+
 params {
   // TODO Need to initialize this
   // igenomes_base = '/scratch/applied-genomics/references/iGenomes/references/'

diff --git a/docs/utd_sysbio.md b/docs/utd_sysbio.md
@@ -12,7 +12,5 @@ module purge
 module load singularity
 ```
 
-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 Sysbio in order to run the pipeline. If in doubt contact OIT.
 >NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact OIT.