add charliecloud.conf

addresses nf-core#824
phue · Jan 11, 2021 · 8c4f1ea · 8c4f1ea
1 parent bb5c10d
commit 8c4f1ea
Show file tree

Hide file tree

Showing 2 changed files with 22 additions and 0 deletions.
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/charliecloud.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/charliecloud.config
@@ -0,0 +1,21 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for Charliecloud
+ * -------------------------------------------------
+ * Assumes that pipeline dependencies are all available in
+ * /opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}/bin
+ * If multiple containers are used, it may be necessary to include their environment
+ * paths in the `env` scope below
+ */
+
+charliecloud {
+  enabled = true
+}
+
+manifest {
+  nextflowVersion = '>=20.12.0-edge'
+}
+
+env {
+  PATH = "/opt/conda/bin:/opt/conda/envs/{{ cookiecutter.name_noslash }}-{{ cookiecutter.version }}/bin:$PATH"
+}
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -74,6 +74,7 @@ profiles {
   podman {
     podman.enabled = true
   }
+  charliecloud { includeConfig 'conf/charliecloud.config' }
   test { includeConfig 'conf/test.config' }
   test_full { includeConfig 'conf/test_full.config' }
 }