Daisybio

.github/workflows/main.yml

@@ -55,6 +55,7 @@ jobs:
           - "crg"
           - "crick"
           - "crukmi"
+          - "daisybio"
           - "denbi_qbic"
           - "dkfz"
           - "ebc"

README.md

@@ -113,6 +113,7 @@ Currently documentation is available for the following systems:
 - [CRICK](docs/crick.md)
 - [Cancer Research UK Manchester Institute](docs/crukmi.md)
 - [CZBIOHUB_AWS](docs/czbiohub.md)
+- [DaiSyBio](docs/daisybio.md)
 - [DENBI_QBIC](docs/denbi_qbic.md)
 - [DKFZ](docs/dkfz.md)
 - [EBC](docs/ebc.md)

conf/daisybio.config

@@ -0,0 +1,31 @@
+params {
+  config_profile_description = 'DaiSyBio cluster profile provided by nf-core/configs.'
+  config_profile_contact = 'Johannes Kersting (Johannes Kersting)'
+  config_profile_url = 'https://biomedical-big-data.de/'
+  max_memory = 1.TB
+  max_cpus = 120
+  max_time = 96.h
+  igenomes_base = '/nfs/data/references/igenomes'
+}
+
+process {
+  executor = 'slurm'
+  queue = 'shared-cpu'
+  maxRetries = 2
+}
+
+executor {
+  queueSize = 30
+  submitRateLimit = '10 sec'
+}
+
+singularity {
+  cacheDir = '/nfs/scratch/singularity_cache'
+}
+
+apptainer {
+  cacheDir = '/nfs/scratch/apptainer_cache'
+}
+
+
+

docs/daisybio.md

@@ -0,0 +1,10 @@
+# nf-core/configs: DaiSyBio
+
+To use the DaiSyBio profile, run a nf-core pipeline with `-profile DaiSyBio,<singularity/apptainer>`.
+
+This will automatically download and apply ['daisybio.config'](../conf/daisybio.config) as a nextflow config file.
+
+The config file will set slurm as a scheduler for the compute cluster, define max resources, and specify cache locations for singularity, apptainer, and iGenomes.
+Pipeline specific parameters still need to be configured manually.
+
+Singularity and apptainer are currently only installed on the exbio nodes. In order to use them, you can either install singularity/apptainer in a conda environment and execute nextflow inside the environment, or limit the queue to exbio nodes with `-process.queue exbio-cpu`

nfcore_custom.config

@@ -37,6 +37,7 @@ profiles {
     crick            { includeConfig "${params.custom_config_base}/conf/crick.config" }
     crukmi           { includeConfig "${params.custom_config_base}/conf/crukmi.config" }
     czbiohub_aws     { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
+    daisybio         { includeConfig "${params.custom_config_base}/conf/daisybio.config" }
     denbi_qbic       { includeConfig "${params.custom_config_base}/conf/denbi_qbic.config" }
     dkfz             { includeConfig "${params.custom_config_base}/conf/dkfz.config" }
     ebc              { includeConfig "${params.custom_config_base}/conf/ebc.config" }