added manifest information to the nextflow.config file to allow for…

… remote execution (#204) - Partial solve to #194 issue

- Deprecation of the `manifest.config´ file
- Add the manifest information to the `nextflow.config` file

changelog.md

@@ -8,6 +8,10 @@
 - `Concoct`: Clustering metagenomic assembled comtigs with coverage and composition
 - `MetaBAT2`: A robust statistical framework for reconstructing genomes from metagenomic data
 
+### Minor/Other changes
+
+- added manifest information to the `nextflow.config` file to allow for remote execution
+
 ## 1.4.1
 
 ### New features

flowcraft/flowcraft.py

@@ -279,10 +279,6 @@ def copy_project(path):
     # Copy bin scripts
     copy_tree(join(repo_dir, "bin"), join(target_dir, "bin"))
 
-    # Copy default config file
-    shutil.copy(join(repo_dir, "nextflow.config"),
-                join(target_dir, "nextflow.config"))
-
     # Copy static profiles file
     shutil.copy(join(repo_dir, "profiles.config"),
                 join(target_dir, "profiles.config"))

flowcraft/generator/engine.py

@@ -150,10 +150,10 @@ class of the component.
         See :func:`NextflowGenerator._get_params_string`
         """
 
-        self.manifest = ""
+        self.config = ""
         """
-        str: Stores de manifest directives string for the nextflow pipeline.
-        See :func:`NextflowGenerator._get_manifest_string`
+        str: Stores de configuration for the nextflow pipeline.
+        See :func:`NextflowGenerator._get_config_string`
         """
 
         self.user_config = ""
@@ -1234,24 +1234,6 @@ def _get_merged_params_help(self):
 
         return help_list
 
-    def _get_manifest_string(self):
-        """Returns the nextflow manifest config string to include in the
-        config file from the information on the pipeline.
-
-        Returns
-        -------
-        str
-            Nextflow manifest configuration string
-        """
-
-        config_str = ""
-
-        config_str += '\n\tname = "{}"'.format(self.pipeline_name)
-        config_str += '\n\tmainScript = "{}"'.format(self.nf_file)
-
-        return config_str
-
-
     @staticmethod
     def _render_config(template, context):
 
@@ -1277,7 +1259,7 @@ def _set_configurations(self):
         resources = ""
         containers = ""
         params = ""
-        manifest = ""
+        config = ""
 
         if self.merge_params:
             params += self._get_merged_params_string()
@@ -1297,8 +1279,6 @@ def _set_configurations(self):
             resources += self._get_resources_string(p.directives, p.pid)
             containers += self._get_container_string(p.directives, p.pid)
 
-        manifest = self._get_manifest_string()
-
         self.resources = self._render_config("resources.config", {
             "process_info": resources
         })
@@ -1308,8 +1288,9 @@ def _set_configurations(self):
         self.params = self._render_config("params.config", {
             "params_info": params
         })
-        self.manifest = self._render_config("manifest.config", {
-            "manifest_info": manifest
+        self.config = self._render_config("nextflow.config", {
+            "pipeline_name": self.pipeline_name,
+            "nf_file": self.nf_file
         })
         self.help = self._render_config("Helper.groovy", {
             "nf_file": basename(self.nf_file),
@@ -1426,9 +1407,9 @@ def write_configs(self, project_root):
         with open(join(project_root, "params.config"), "w") as fh:
             fh.write(self.params)
 
-        # Write manifest config
-        with open(join(project_root, "manifest.config"), "w") as fh:
-            fh.write(self.manifest)
+        # Write nextflow config
+        with open(join(project_root, "nextflow.config"), "w") as fh:
+            fh.write(self.config)
 
         # Write user config if not present in the project directory
         if not exists(join(project_root, "user.config")):

flowcraft/nextflow.config → flowcraft/generator/templates/nextflow.config

@@ -1,3 +1,8 @@
+manifest {
+    name = "{{ pipeline_name }}"
+    mainScript = "{{ nf_file }}"
+}
+
 params {
     platformHTTP = null
     reportHTTP = null
@@ -172,5 +177,4 @@ includeConfig "profiles.config"
 includeConfig "resources.config"
 includeConfig "containers.config"
 includeConfig "params.config"
-includeConfig "manifest.config"
 includeConfig "user.config"

flowcraft/tests/test_assemblerflow.py

@@ -53,7 +53,7 @@ def test_build_file_2(tmp):
 
     assert sorted(os.listdir(tmp)) == [".forkTree.json", ".treeDag.json",
                                        "containers.config",
-                                       "lib", "manifest.config", "params.config",
+                                       "lib", "nextflow.config", "params.config",
                                        "resources.config", "teste.html",
                                        "teste.nf", "user.config"]