Add proteinfold-specific CRG config

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/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 -->

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" }
+}