Update for the daisybio profile

conf/daisybio.config

@@ -1,30 +1,65 @@
 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/'
+    config_profile_contact = 'Johannes Kersting (@JohannesKersting)'
+    config_profile_url = 'https://www.mls.ls.tum.de/daisybio/startseite/'
     max_memory = 1.TB
     max_cpus = 120
     max_time = 96.h
     igenomes_base = '/nfs/data/references/igenomes'
 }
 
+// define workDir in /nfs/scratch/nf-core_work/ named after the launch dir
+def work_dir = "/nfs/scratch/nf-core_work/"
+if(new File(work_dir).exists() && System.getenv("PWD")) {
+        workDir = work_dir+System.getenv("PWD").tokenize('/').join('.')
+}
+
 process {
     executor = 'slurm'
     queue = 'shared-cpu'
     maxRetries = 2
 }
 
 executor {
-    queueSize = 30
+    queueSize = 50
     submitRateLimit = '10 sec'
 }
 
-singularity {
-    cacheDir = '/nfs/scratch/singularity_cache'
-}
+cleanup = true
+profiles {
+    // profile to keep work directory
+    keep_work {
+        cleanup = false
+    }
+
+    //profile for singularity
+    singularity {
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        process.beforeScript = 'module load singularity'
+        singularity.cacheDir = '/nfs/scratch/singularity_cache'
+    }
+
+    // profile for apptainer
+    apptainer {
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        process.beforeScript = 'module load apptainer'
+        apptainer.cacheDir = '/nfs/scratch/apptainer_cache'
+    }
 
-apptainer {
-    cacheDir = '/nfs/scratch/apptainer_cache'
 }
 
 

docs/daisybio.md

@@ -5,6 +5,6 @@ To use the DaiSyBio profile, run a nf-core pipeline with `-profile daisybio,<sin
 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.
+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`
+Work directories will be kept at `/nfs/scratch/nf-core_work/` in a directory named after the full path of the launch directory ("." separated). Thy are automatically removed after a successful pipeline run. To keep the intermediate file, e.g. for using the `-resume` function, add `keep_work` as a profile: `-profile daisybio,<singularity/apptainer>,keep_work`.