Merge pull request #430 from athbaltzis/master

Add proteinfold-specific CRG config

.github/workflows/main.yml

@@ -49,6 +49,7 @@ jobs:
           - "cfc_dev"
           - "cheaha"
           - "computerome"
+          - "crg"
           - "crick"
           - "crukmi"
           - "denbi_qbic"

README.md

@@ -228,6 +228,8 @@ Currently documentation is available for the following pipelines within specific
 - taxprofiler
   - [EVA](docs/pipeline/taxprofiler/eva.md)
   - [hasta](docs/pipeline/taxprofiler/hasta.md)
+- proteinfold
+  - [CRG](docs/pipeline/proteinfold/crg.md)
 
 ### Pipeline-specific documentation
 

conf/crg.config

@@ -0,0 +1,14 @@
+//Profile config names for nf-core/configs
+params {
+  config_profile_description = 'Centre for Genomic Regulation (CRG) cluster profile provided by nf-core/configs'
+  config_profile_contact = 'Athanasios Baltzis (@athbaltzis)'
+  config_profile_url = 'http://www.linux.crg.es/index.php/Main_Page'
+}
+
+process {
+  executor = 'crg'
+}
+
+singularity {
+  enabled = true
+}

conf/pipeline/proteinfold/crg.config

@@ -0,0 +1,27 @@
+profiles {
+    crg {
+        params {
+            config_profile_contact = 'Athanasios Baltzis (@athbaltzis)'
+            config_profile_description = 'nf-core/proteinfold CRG profile provided by nf-core/configs'
+        }
+        executor.name = 'crg'
+        process {
+            queue = 'short-sl7,long-sl7'
+            withName: 'RUN_AF2|RUN_AF2_PRED|COLABFOLD_BATCH' {
+                cpus = 1
+                memory = "30 GB"
+                queue = params.use_gpu ? 'gpu' : 'long-sl7'
+                clusterOptions = { ( task.queue == 'gpu' ? '-l gpu=1' : '' ) }
+            }
+            withName: 'ARIA2' {
+                time = '12h'
+            }
+            withName: 'MMSEQS_COLABFOLDSEARCH' {
+                queue = 'mem_512'
+                memory = "100 GB"
+                cpus = 8
+                time = '12h'
+            }
+        }
+    }
+}

docs/pipeline/proteinfold/crg.md

@@ -0,0 +1,23 @@
+# nf-core/configs: CRG proteinfold specific configuration
+
+Extra specific configuration for proteinfold pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile crg`.
+
+This will download and launch the proteinfold specific [`crg.config`](../../../conf/pipeline/proteinfold/crg.config) which has been pre-configured with a setup suitable for the sge cluster.
+
+Example: `nextflow run nf-core/proteinfold -profile crg`
+
+## proteinfold specific configurations for CRG
+
+Specific configurations for CRG has been made for proteinfold.
+
+### General profiles
+
+<!-- TODO -->
+
+### Contextual profiles
+
+<!-- TODO -->

nfcore_custom.config

@@ -30,6 +30,7 @@ profiles {
   cfc_dev      { includeConfig "${params.custom_config_base}/conf/cfc_dev.config" }
   cheaha       { includeConfig "${params.custom_config_base}/conf/cheaha.config" }
   computerome  { includeConfig "${params.custom_config_base}/conf/computerome.config" }
+  crg         { includeConfig "${params.custom_config_base}/conf/crg.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
   crukmi       { includeConfig "${params.custom_config_base}/conf/crukmi.config" }
   czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }

pipeline/proteinfold.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/proteinfold custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/proteinfold folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  crg { includeConfig "${params.custom_config_base}/conf/pipeline/proteinfold/crg.config" }
+}