Merge pull request #708 from nf-core/feature/danhead

[WIP]: danhead @ KU

.github/workflows/main.yml

@@ -95,7 +95,7 @@ jobs:
           - "janelia"
           - "jax"
           - "jex"
-          - "ku_sund_dangpu"
+          - "ku_sund_danhead"
           - "leicester"
           - "lugh"
           - "m3c"

README.md

@@ -147,7 +147,7 @@ Currently documentation is available for the following systems:
 - [Janelia Research Campus](docs/janelia.md)
 - [JAX](docs/jax.md)
 - [Jex](docs/jex.md)
-- [KU SUND DANGPU](docs/ku_sund_dangpu.md)
+- [KU SUND DANHEAD](docs/ku_sund_danhead.md)
 - [LUGH](docs/lugh.md)
 - [M3C](docs/m3c.md)
 - [MAESTRO](docs/maestro.md)

conf/ku_sund_danhead.config

@@ -0,0 +1,43 @@
+params {
+
+    config_profile_contact = 'Adrija Kalvisa <[email protected]>'
+    config_profile_description = 'danhead01fl configuration'
+    config_profile_url = ''
+
+    max_cpus = 8
+    max_memory = 64.GB
+    max_time = 72.h
+}
+
+cleanup = true
+
+singularity {
+    enabled = true
+    autoMounts = true
+    runOptions = '--bind /projects:/projects'
+}
+
+process {
+    executor = 'slurm'
+    containerOptions = "--env NUMBA_CACHE_DIR=/tmp/numbacache"
+    withName: SRATOOLS_PREFETCH {
+        ext.args = '--max-size 60g'
+    }
+}
+
+executor {
+    queueSize = 5
+    submitRateLimit = '30/1min'
+}
+
+profiles {
+    dancmpn01fl {
+        process.clusterOptions = '-w dancmpn01fl'
+    }
+    dancmpn02fl {
+        process.clusterOptions = '-w dancmpn02fl'
+    }
+    dangpu01fl {
+        process.clusterOptions = '-p gpuqueue'
+    }
+}

conf/pipeline/methylseq/ku_sund_dangpu.config → conf/pipeline/methylseq/ku_sund_danhead.config

@@ -1,6 +1,6 @@
 params {
     config_profile_contact = 'Adrija Kalvisa (@adrijak)'
-    config_profile_description = 'nf-core/methylseq ku_sund_dangpu profile provided by nf-core/configs'
+    config_profile_description = 'nf-core/methylseq ku_sund_danhead profile provided by nf-core/configs'
 
     // methylseq usually runs extremely long hours, use 2x the normal max_time allowance for this pipeline
     max_time = 144.h

docs/ku_sund_danhead.md

@@ -0,0 +1,47 @@
+# nf-core/configs: ku_sund_danhead configuration
+
+All nf-core pipelines have been successfully configured for use on the DanHead server
+at the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW) at the University of Copenhagen.
+The server consists of two computing nodes and one GPU node.
+
+To use the institution profile, run the pipeline with `-profile ku_sund_danhead`.
+This will download and launch the [`ku_sund_danhead.config`](../conf/ku_sund_danhead.config)
+which has been pre-configured with a setup suitable for the DANGPU.
+
+## Environment variables
+
+The main environment variables for nextflow are specified in `/projects/dan1/apps/etc/bashrc`.
+
+## 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. `-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 `nf-core/rnaseq` on **dancmpn01fl**:
+
+```bash
+#!/bin/bash
+
+#SBATCH --job-name=test
+#SBATCH --mail-type=END,FAIL
+#SBATCH --mail-user=NONE
+#SBATCH -c 1
+#SBATCH --mem=2gb
+#SBATCH --time=1-00:00:00
+#SBATCH --output=test.log
+#SBATCH -w dancmpn01fl
+
+module load openjdk/20.0.0 nextflow/23.04.1.5866 singularity/3.8.0
+
+nextflow run nf-core/rnaseq \
+  -profile test,ku_sund_danhead,dancmpn01fl \
+  --input <name-of-input-csv-file> \
+  --outdir <name-of-output-directory>
+
+```
+
+To run it on **dancmpn02fl** change `#SBATCH -w dancmpn02fl` and
+`-profile test,ku_sund_danhead,dancmpn02fl`

nfcore_custom.config

@@ -71,7 +71,7 @@ profiles {
     janelia            { includeConfig "${params.custom_config_base}/conf/janelia.config" }
     jax                { includeConfig "${params.custom_config_base}/conf/jax.config" }
     jex                { includeConfig "${params.custom_config_base}/conf/jex.config" }
-    ku_sund_dangpu     { includeConfig "${params.custom_config_base}/conf/ku_sund_dangpu.config"}
+    ku_sund_danhead    { includeConfig "${params.custom_config_base}/conf/ku_sund_danhead.config"}
     leicester          { includeConfig "${params.custom_config_base}/conf/leicester.config" }
     lugh               { includeConfig "${params.custom_config_base}/conf/lugh.config" }
     m3c                { includeConfig "${params.custom_config_base}/conf/m3c.config" }