Merge pull request #516 from nevinwu/master

Create incliva.config

.github/workflows/main.yml

@@ -71,6 +71,7 @@ jobs:
           - "icr_davros"
           - "ifb_core"
           - "imperial"
+          - "incliva"
           - "ipop_up"
           - "janelia"
           - "jax"

README.md

@@ -128,6 +128,7 @@ Currently documentation is available for the following systems:
 - [ICR_DAVROS](docs/icr_davros.md)
 - [IFB](docs/ifb_core.md)
 - [IMPERIAL](docs/imperial.md)
+- [INCLIVA](docs/incliva.md)
 - [iPOP-UP](docs/ipop_up.md)
 - [Janelia Research Campus](docs/janelia.md)
 - [JAX](docs/jax.md)

conf/incliva.config

@@ -0,0 +1,52 @@
+// Profile details
+params {
+    config_profile_description = 'INCLIVA Health Research Institute profile for nf-core.'
+    config_profile_contact = 'Sheila Zúñiga Trejos - [email protected]'
+    config_profile_url = 'https://www.incliva.es/en/services/platforms/bioinformatics-unit/'
+}
+
+// Function to get hostname
+def getHostname() {
+    def process = 'hostname'.execute()
+    process.waitFor()
+    return process.text.trim()
+}
+
+// Function to set singularity path according to which host nextflow is running on
+def setHostConfig(String hostname) {
+    if (hostname == 'vlinuxcervantes3srv') {
+        System.out.println("\nINFO: working on ${hostname}\n")
+
+        // Resources details
+        params.max_memory = 60.GB
+        params.max_cpus = 15
+        singularity.cacheDir =  "/nfs/home/software/singularity/nf_cacheDir"
+
+    } else if (hostname == 'vlinuxcervantes4srv') {
+        System.out.println("\nINFO: working on ${hostname}.\n")
+
+        // Resources details
+        params.max_memory = 120.GB
+        params.max_cpus = 19
+        singularity.cacheDir = "/nfs/home/software/singularity/nf_cacheDir"
+
+    } else {
+        System.err.println("\nERROR: unknown machine. Update incliva.config on nf-core/configs if you are working on another host.\n")
+    }
+}
+
+def hostname = getHostname()
+
+setHostConfig(hostname)
+
+// Singularity details
+singularity {
+    enabled = true
+    autoMounts = true
+}
+
+// Process details
+process {
+    executor = 'local'
+    maxRetries = 2
+}

docs/incliva.md

@@ -0,0 +1,14 @@
+# nf-core/configs: INCLIVA Configuration
+
+All nf-core pipelines have been successfully configured for use on the vlinuxcervantes3 & vlinuxcervantes4 servers at the INCLIVA Health Research Institute. Using this config file will automatically detect which one you are working on, so you do not need to specify it yourself.
+
+To use, run the pipeline with `-profile incliva`. This will download and launch the [`incliva.config`](../conf/incliva.config) which has been pre-configured with a setup suitable for the vlinuxcervantes3 & vlinuxcervantes4 servers. When using this profile, if Singularity images have not been downloaded already, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline. Downloaded images can be checked in the singularity_path directory defined in the config file.
+
+## Running the workflow on the INCLIVA vlinuxcervantes3 & vlinuxcervantes4 servers
+
+Nextflow and Singularity are needed to run any nf-core workflow:
+
+- Install Nextflow : [here](https://www.nextflow.io/docs/latest/getstarted.html#)
+- Install Singularity : [here](https://docs.sylabs.io/guides/3.0/user-guide/installation.html)
+
+By default, Nextflow uses the local executor. The processes are parallelised by spawning multiple threads, taking advantage of the multi-core architecture of the CPU.

nfcore_custom.config

@@ -53,6 +53,7 @@ profiles {
     icr_davros       { includeConfig "${params.custom_config_base}/conf/icr_davros.config" }
     ifb_core         { includeConfig "${params.custom_config_base}/conf/ifb_core.config" }
     imperial         { includeConfig "${params.custom_config_base}/conf/imperial.config" }
+    incliva          { includeConfig "${params.custom_config_base}/conf/incliva.config" }
     ipop_up          { includeConfig "${params.custom_config_base}/conf/ipop_up.config" }
     janelia          { includeConfig "${params.custom_config_base}/conf/janelia.config" }
     jax              { includeConfig "${params.custom_config_base}/conf/jax.config" }