Merge pull request #416 from jfy133/master

Add HKI cluster

.github/workflows/main.yml

@@ -62,6 +62,7 @@ jobs:
           - "google"
           - "hasta"
           - "hebbe"
+          - "hki"
           - "icr_davros"
           - "ifb_core"
           - "imperial"

README.md

@@ -118,6 +118,7 @@ Currently documentation is available for the following systems:
 - [GOOGLE](docs/google.md)
 - [HASTA](docs/hasta.md)
 - [HEBBE](docs/hebbe.md)
+- [HKI](docs/hki.md)
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IMPERIAL](docs/imperial.md)
 - [JAX](docs/jax.md)

conf/hki.config

@@ -0,0 +1,104 @@
+params {
+  config_profile_description = 'HKI clusters profile provided by nf-core/configs.'
+  config_profile_contact = 'James Fellows Yates (@jfy133)'
+  config_profile_url = 'https://leibniz-hki.de'
+}
+
+profiles {
+    apate {
+        params {
+            config_profile_description = 'apate HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 128.GB
+            max_cpus = 32
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    aither {
+        params {
+            config_profile_description = 'aither HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 128.GB
+            max_cpus = 32
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    arges {
+        params {
+            config_profile_description = 'arges HKI cluster profile provided by nf-core/configs'
+            config_profile_contact = 'James Fellows Yates (@jfy133)'
+            config_profile_url = 'https://leibniz-hki.de'
+            max_memory = 64.GB
+            max_cpus = 12
+            max_time = 1440.h
+        }
+        process {
+            executor = 'local'
+            maxRetries = 2
+        }
+
+        executor {
+            queueSize = 8
+        }
+
+        singularity {
+            enabled = true
+            autoMounts = true
+            cacheDir = '/Net/Groups/ccdata/apps/singularity'
+        }
+
+        conda {
+            cacheDir = '/Net/Groups/ccdata/apps/conda_envs'
+        }
+
+        cleanup = true
+    }
+
+    debug {
+        cleanup = false
+    }
+}

docs/hki.md

@@ -0,0 +1,24 @@
+# nf-core/configs: HKI Configuration
+
+All nf-core pipelines have been successfully configured for use on clusters at the [Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute](https://www.leibniz-hki.de/en).
+
+To use, run the pipeline with `-profile hki,<cluster>`. This will download and launch the [`hki.config`](../conf/hki.config) which contains specific profiles for each cluster. The number of parallel jobs that run is currently limited to 8.
+
+The currently available profiles are:
+
+- apate (uses singularity, cleanup set to true by default)
+- arges (uses singularity, cleanup set to true by default)
+- aither (uses singularity, cleanup set to true by default)
+- debug (sets cleanup to false for debugging purposes, use e.g. `profile hki,<cluster>,debug`)
+
+Note that Nextflow is not necessarily installed by default on the HKI HPC cluster(s). You will need to install it into a directory you have write access to.
+Follow these instructions from the Nextflow documentation.
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+
+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 HKI HPC clusters in order to run the pipeline. If in doubt contact the ICT Service Desk.
+> NB: Nextflow will need to submit the jobs via SLURM to the HKI HPC clusters and as such the commands above will have to be executed on the login
+> node. If in doubt contact ICT.

nfcore_custom.config

@@ -44,6 +44,7 @@ profiles {
   google       { includeConfig "${params.custom_config_base}/conf/google.config" }
   hasta        { includeConfig "${params.custom_config_base}/conf/hasta.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
+  hki          { includeConfig "${params.custom_config_base}/conf/hki.config"}
   icr_davros   { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }