Merge branch 'nf-core:master' into sbc_sharc

.github/workflows/main.yml

@@ -67,6 +67,7 @@ jobs:
           - "ifb_core"
           - "imperial"
           - "jax"
+          - "ku_sund_dangpu"
           - "lugh"
           - "marvin"
           - "medair"

README.md

@@ -122,6 +122,7 @@ Currently documentation is available for the following systems:
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IMPERIAL](docs/imperial.md)
 - [JAX](docs/jax.md)
+- [KU SUND DANGPU](docs/ku_sund_dangpu.md)
 - [LUGH](docs/lugh.md)
 - [MAESTRO](docs/maestro.md)
 - [MARVIN](docs/marvin.md)

conf/cheaha.config

@@ -9,7 +9,7 @@ params {
 }
 
 env {
-    TMPDIR="$USER"
+    TMPDIR="$scratch_dir"
     SINGULARITY_TMPDIR="$scratch_dir"
 }
 

conf/ku_sund_dangpu.config

@@ -0,0 +1,25 @@
+params {
+  config_profile_contact = 'Adrija Kalvisa <adrija.kalvisa@sund.ku.dk>'
+  config_profile_description = 'dangpufl01 configuration'
+  config_profile_url = ''
+  
+  // General cpus/memory/time requirements
+  max_cpus = 30
+  max_memory = 200.GB
+  max_time = 72.h
+}
+
+process {
+  executor = 'slurm'
+  
+}
+
+executor {
+  queueSize = 5
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '--bind /projects:/projects'
+}

docs/ku_sund_dangpu.md

@@ -0,0 +1,35 @@
+# nf-core/configs: ku_sund_dangpu configuration
+
+All nf-core pipelines have been successfully configured for use on the DANGPU at the
+Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) and the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen.
+
+To use, run the pipeline with `-profile ku_sund_dangpu`. This will download and launch the [`ku_sund_dangpu.config`](../conf/ku_sund_dangpu.config) which has been pre-configured with a setup suitable for the DANGPU.
+
+## Modules
+
+Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on DANGPU. You can do this by issuing the commands below:
+
+```bash
+## Load Nextflow and Singularity environment modules
+module purge
+module load java/11.0.15 nextflow/22.04.4 singularity/3.8.0
+# alternative modules for older nextflow version (v.21) that works with java 8:
+# module load jdk/1.8.0_291 nextflow/21.04.1.5556 singularity/3.8.0
+export NXF_OPTS='-Xms1g -Xmx4g'
+export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
+export NXF_TEMP=/scratch/tmp
+export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
+```
+
+Create the user-specific nextflow directories if they don't exist yet:
+
+```
+mkdir $NXF_SINGULARITY_CACHEDIR
+mkdir $NXF_HOME
+```
+
+Finally, download and test the pipeline of choice using the `-profile ku_sund_dangpu`. Note that normally you would run resource-intensive commands with slurm, but in case of nf-core pipelines you do not have to do this: we have pre-configured slurm to be the resource manager within the `ku_sund_dangpu profile`. Just make sure that the pipeline is run within a tmux session.
+
+```
+nextflow run nf-core/rnaseq -profile test,ku_sund_dangpu
+```

nfcore_custom.config

@@ -49,6 +49,7 @@ profiles {
   ifb_core     { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
   imperial     { includeConfig "${params.custom_config_base}/conf/imperial.config" }
   jax          { includeConfig "${params.custom_config_base}/conf/jax.config" }
+  ku_sund_dangpu {includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
   lugh         { includeConfig "${params.custom_config_base}/conf/lugh.config" }
   maestro      { includeConfig "${params.custom_config_base}/conf/maestro.config" }
   marvin       { includeConfig "${params.custom_config_base}/conf/marvin.config" }