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Merge pull request #410 from nf-core/chear-var-fix

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Fix cheaha config due to use of environmental variable
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Maxime U. Garcia 2022-09-01 11:13:37 +02:00 committed by GitHub
commit ebcc3d278f
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1 changed files with 6 additions and 3 deletions
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9
conf/cheaha.config
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@ -1,3 +1,6 @@
// Define the Scratch directory
def scratch_dir = System.getenv("USER_SCRATCH") ?: "/tmp"
params { params {
config_profile_name = 'cheaha' config_profile_name = 'cheaha'
config_profile_description = 'University of Alabama at Birmingham Cheaha HPC' config_profile_description = 'University of Alabama at Birmingham Cheaha HPC'
@ -6,14 +9,14 @@ params {
} }
env { env {
TMPDIR="$USER_SCRATCH" TMPDIR="$USER"
SINGULARITY_TMPDIR="$USER_SCRATCH" SINGULARITY_TMPDIR="$scratch_dir"
} }
singularity { singularity {
enabled = true enabled = true
autoMounts = true autoMounts = true
runOptions = "--contain --workdir $USER_SCRATCH" runOptions = "--contain --workdir $scratch_dir"
} }
process { process {