Merge pull request #422 from giusmar/master

Add TIGEM config file

.github/workflows/main.yml

@@ -88,6 +88,7 @@ jobs:
           - "sanger"
           - "sbc_sharc"
           - "seg_globe"
+          - "tigem"
           - "uct_hpc"
           - "unibe_ibu"
           - "uppmax"

README.md

@@ -142,6 +142,7 @@ Currently documentation is available for the following systems:
 - [SANGER](docs/sanger.md)
 - [SBC_SHARC](docs/sbc_sharc.md)
 - [SEG_GLOBE](docs/seg_globe.md)
+- [TIGEM](docs/tigem.md)
 - [UCT_HPC](docs/uct_hpc.md)
 - [UNIBE_IBU](docs/unibe_ibu.md)
 - [UPPMAX](docs/uppmax.md)

conf/tigem.config

@@ -0,0 +1,14 @@
+params {
+  config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
+  config_profile_contact = 'Giuseppe Martone (@giusmar)'
+  config_profile_url = 'https://github.com/giusmar'
+}
+
+process.executor = 'slurm'
+google.zone = 'europe-west1'
+
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = 'work/singularity'
+}

docs/tigem.md

@@ -0,0 +1,7 @@
+# nf-core/configs: TIGEM configuration
+
+To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
+
+---
+
+This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.

nfcore_custom.config

@@ -70,6 +70,7 @@ profiles {
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   sbc_sharc    { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
+  tigem        { includeConfig "${params.custom_config_base}/conf/tigem.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }