diff ui/assets/config/executor/biowulf_cluster.config @ 0:d9c5c5b87fec draft

planemo upload for repository https://github.com/ncbi/egapx commit 8173d01b08d9a91c9ec5f6cb50af346edc8020c4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ui/assets/config/executor/biowulf_cluster.config	Sat Aug 03 11:16:53 2024 +0000
@@ -0,0 +1,51 @@
+// Config for https://hpc.nih.gov/
+// This config doesn't use profiles because EGAPx can't use them now.
+// It is a copy of 'biowulf' profile from config at https://hpc.nih.gov/apps/nextflow.html
+
+params {
+  config_profile_description = 'Biowulf nf-core config'
+  config_profile_contact = '[e-mail]'
+  config_profile_url = 'https://hpc.nih.gov/apps/nextflow.html'
+  max_memory = '224 GB'
+  max_cpus = 32
+  max_time = '72 h'
+
+  igenomes_base = '/fdb/igenomes_nf/'
+}
+
+
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = "/data/$USER/singularity"
+    envWhitelist='https_proxy,http_proxy,ftp_proxy,DISPLAY,SLURM_JOB_ID,SINGULARITY_BINDPATH'
+}
+
+env {
+    SINGULARITY_CACHEDIR="/data/$USER/singularity"
+    PYTHONNOUSERSITE = 1
+}
+
+process {
+    executor = 'slurm'
+    maxRetries = 1
+    queue = 'norm'
+    queueSize = 200
+    pollInterval = '2 min'
+    queueStatInterval = '5 min'
+    submitRateLimit = '6/1min'
+    retry.maxAttempts = 1
+
+    clusterOptions = ' --gres=lscratch:200 '
+
+    scratch = '/lscratch/$SLURM_JOB_ID'
+    // with the default stageIn and stageOut settings using scratch can
+    // result in humungous work folders
+    // see https://github.com/nextflow-io/nextflow/issues/961 and
+    //     https://www.nextflow.io/docs/latest/process.html?highlight=stageinmode
+    stageInMode = 'symlink'
+    stageOutMode = 'rsync'
+    
+    // for running pipeline on group sharing data directory, this can avoid inconsistent files timestamps
+    cache = 'lenient'
+}
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