Merge pull request #833 from luisas/add-multiplesequencealign

add Multiplesequencealign CRG specific config

README.md

@@ -285,6 +285,8 @@ Currently documentation is available for the following pipelines within specific
   - [EVA](docs/pipeline/mag/eva.md)
 - methylseq
   - [FUB Curta](docs/pipeline/methylseq/fub_curta.md)
+- multiplesequencealign
+  - [CRG](docs/pipeline/multiplesequencealign/crg.md)
 - rnafusion
   - [HASTA](docs/pipeline/rnafusion/hasta.md)
   - [MUNIN](docs/pipeline/rnafusion/munin.md)

conf/pipeline/multiplesequencealign/crg.config

@@ -0,0 +1,18 @@
+profiles {
+    crg {
+        params {
+            config_profile_contact     = 'Luisa Santus (@luisas)'
+            config_profile_description = 'nf-core/multiplesequencealign CRG profile provided by nf-core/configs'
+        }
+        executor.name = 'crg'
+        process {
+            queue = 'short-centos79,long-centos79'
+            withName: 'LEARNMSA_ALIGN' {
+                cpus           = 8
+                memory         = "30 GB"
+                queue          = params.use_gpu ? 'gpu' : 'long-centos79'
+                clusterOptions = { (task.queue == 'gpu' ? '-l gpu=1,virtual_free=30G' : '') }
+            }
+        }
+    }
+}

docs/pipeline/multiplesequencealign/crg.md

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

pipeline/multiplesequencealign.config

@@ -9,4 +9,7 @@
  */
 
 profiles {
+    crg {
+        includeConfig "${params.custom_config_base}/conf/pipeline/multiplesequencealign/crg.config"
+    }
 }