update institution profile for KU_SUND_DANGPU

conf/ku_sund_dangpu.config

@@ -4,8 +4,8 @@ params {
   config_profile_url = ''
 
   // General cpus/memory/time requirements
-  max_cpus = 30
-  max_memory = 200.GB
+  max_cpus = 8
+  max_memory = 64.GB
   max_time = 72.h
 }
 
@@ -22,4 +22,4 @@ singularity {
   enabled = true
   autoMounts = true
   runOptions = '--bind /projects:/projects'
-}
+}

docs/ku_sund_dangpu.md

@@ -1,9 +1,8 @@
 # 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.
+All nf-core pipelines have been successfully configured for use on the DANGPU server at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) 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.
+To use the institution profile, 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.
 
 ## Prepare the environment
 
@@ -19,12 +18,12 @@ Within the created session load Nextflow and Singularity and set up the environm
 ```bash
 ## Load Nextflow and Singularity environment modules
 module purge
-module load java/11.0.15 nextflow/22.04.4 singularity/3.8.0
+module load dangpu_libs java/11.0.15 nextflow/22.10.6 singularity/3.8.0 python/3.7.13 nf-core/2.7.2
 
 # set up bash environment variables for memory
 export NXF_OPTS='-Xms1g -Xmx4g'
 export NXF_HOME=/projects/dan1/people/${USER}/cache/nxf-home
-export NXF_TEMP=/scratch/tmp/${USER}
+export NXF_TEMP=/scratch/temp/${USER}
 export NXF_SINGULARITY_CACHEDIR=/projects/dan1/people/${USER}/cache/singularity-images
 ```
 
@@ -38,20 +37,44 @@ mkdir $NXF_TEMP
 
 ## How to run a pipeline with institution profile
 
-To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline.
+To download and test a pipeline for the first time, use the `-profile test` and specify `--outdir`. It is a good practice to use the pipeline version with specifying `-r` each time you run a pipeline. `-r` refers to a revision version and is useful to ensure reproducibility when rerunning the pipeline. You can read more on nf-core pipeline reproducibility [here](https://nf-co.re/rnaseq/3.10.1/usage#reproducibility)
 
 For example to run rnaseq:
 
 ```
-nextflow run nf-core/rnaseq -r 3.8.1 -profile test,ku_sund_dangpu --outdir <name-of-output-directory>
+nextflow run nf-core/rnaseq -r 3.10.1 -profile test,ku_sund_dangpu --outdir <name-of-output-directory>
 ```
 
 To run a pipeline:
 
 ```
-nextflow run nf-core/rnaseq  -r 3.8.1 -profile ku_sund_dangpu --outdir <name-of-output-directory>
+nextflow run nf-core/rnaseq  -r 3.10.1 -profile ku_sund_dangpu --outdir <name-of-output-directory> --input <name-of-input-csv-file>
 ```
 
 ## Notes
 
 Note that normally on dangpu server you are required to run resource-intensive commands with slurm, but at ku_sund_dangpu profile 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 or within a screen session.
+
+Start a new session and enter the vitual screen named `mysessionname`:
+
+```bash
+tmux new-session -s mysessionname
+
+# load modules
+# define variables
+# run nfcore pipeline here
+```
+
+Detach a session use control+B and then press d.
+
+To attach a previously detached session again:
+
+```bash
+tmux atttach-session -t mysessionname
+```
+
+To exit a tmux session when the job is done:
+
+```bash
+exit
+```