From a63ca751ee74778de4c22985f1cf44ec33e1d197 Mon Sep 17 00:00:00 2001
From: lecorguille <gildas.le.corguille@gmail.com>
Date: Thu, 22 Oct 2020 16:57:41 +0200
Subject: [PATCH] Add ABiMS

---
 conf/abims.config | 24 ++++++++++++++++++++++++
 docs/abims.md     | 46 ++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 conf/abims.config
 create mode 100644 docs/abims.md

diff --git a/conf/abims.config b/conf/abims.config
new file mode 100644
index 0000000..47be8cd
--- /dev/null
+++ b/conf/abims.config
@@ -0,0 +1,24 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'The ABiMS cluster profile'
+  config_profile_contact = 'Gildas Le Corguillé (@lecorguille)'
+  config_profile_url = 'https://abims.sb-roscoff.fr'
+}
+
+singularity {
+  enabled = true
+  autoMounts = true
+  runOptions = '-B /scratch:/scratch -B /scratch2:/scratch2 -B /shared:/shared'
+}
+
+process {
+  executor = 'slurm'
+}
+
+params {
+  igenomes_ignore = true
+  igenomesIgnore = true //deprecated
+  max_memory = 750.GB
+  max_cpus = 200
+  max_time = 24.h
+}
diff --git a/docs/abims.md b/docs/abims.md
new file mode 100644
index 0000000..a3298e5
--- /dev/null
+++ b/docs/abims.md
@@ -0,0 +1,46 @@
+# nf-core/configs: ABiMS Configuration
+
+All nf-core pipelines have been successfully configured for use on the ABiMS cluster.
+
+To use, run the pipeline with `-profile abims`. This will download and launch the [`abims.config`](../conf/abims.config) which has been pre-configured with a setup suitable for the ABiMS cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+## Request an account
+You will need an account to use the HPC cluster on ABiMS in order
+to run the pipeline. If in doubt see [http://abims.sb-roscoff.fr/account](http://abims.sb-roscoff.fr/account).
+
+## Running the workflow on the ABiMS cluster
+
+Nextflow is installed on the ABiMS cluster. Some documentation is available on the [ABiMS website](http://abims.sb-roscoff.fr/resources/cluster/howto#nextflow).
+
+You need to activate it like this:
+
+```bash
+module load nextflow/20.04.1 slurm-drmaa/1.0.8
+```
+
+Nextflow manages each process as a separate job that is submitted to the cluster by using the sbatch command.
+Nextflow shouldn't run directly on the submission node but on a compute node. Run nextflow from a compute node:
+
+```bash
+# Login to a compute node
+srun --pty bash
+
+# Load the dependencies if not done before
+module load nextflow/20.04.1 slurm-drmaa/1.0.8
+
+# Run a downloaded/git-cloned nextflow workflow from
+nextflow run \\
+/path/to/nf-core/workflow \\
+-resume
+-profile abims \\
+--email my-email@example.org  \\
+-c my-specific.config
+...
+
+# Or use the nf-core client
+nextflow run nf-core/rnaseq ...
+```
+
+## Databanks
+
+A local copy of several genomes are available in `/shared/bank` directory.