Refgenie alias translation

CHANGELOG.md

@@ -42,6 +42,7 @@
 - Use `nfcore/gitpod:dev` container in the dev branch ([#2196](https://github.com/nf-core/tools/pull/2196))
 - Replace requests_mock with responses in test mocks ([#2165](https://github.com/nf-core/tools/pull/2165)).
 - Add warning when installing a module from an `org_path` that exists in multiple remotes in `modules.json` ([#2228](https://github.com/nf-core/tools/pull/2228) [#2239](https://github.com/nf-core/tools/pull/2239)).
+- Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file ([#2242](https://github.com/nf-core/tools/pull/2242)).
 
 ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19]
 

nf_core/refgenie.py

@@ -2,6 +2,7 @@
 Update a nextflow.config file with refgenie genomes
 """
 
+import json
 import logging
 import os
 import re
@@ -10,6 +11,7 @@
 
 import rich
 import rich.traceback
+import yaml
 
 import nf_core.utils
 
@@ -45,6 +47,7 @@ def _print_nf_config(rgc):
     """
     abg = rgc.list_assets_by_genome()
     genomes_str = ""
+    alias_translations = _get_alias_translation_file(rgc)
     for genome, asset_list in abg.items():
         genomes_str += f"    '{genome}' {{\n"
         for asset in asset_list:
@@ -54,6 +57,10 @@ def _print_nf_config(rgc):
             except Exception:
                 log.warning(f"{genome}/{asset} is incomplete, ignoring...")
             else:
+                # Translate an alias name to the alias used in the pipeline
+                if asset in alias_translations.keys():
+                    log.info(f"Translating refgenie asset alias {asset} to {alias_translations[asset]}.")
+                    asset = alias_translations[asset]
                 genomes_str += f'      {asset.ljust(20, " ")} = "{pth}"\n'
         genomes_str += "    }\n"
 
@@ -100,6 +107,38 @@ def _update_nextflow_home_config(refgenie_genomes_config_file, nxf_home):
             log.info(f"Created new nextflow config file: {nxf_home_config}")
 
 
+def _get_alias_translation_file(rgc):
+    """
+    Read a file containing alias translations.
+
+    Alias translation file should be located in the same folder as the refgenie `genome_config.yaml` file,
+    the path is set to $REFGENIE environment variable by `refgenie init`.
+    Alias translation file should be named `alias_translations.yaml`
+
+    Input file contains the name of refgenie server aliases as keys and the name of the respective nf-core pipeline aliases as values.
+    Such as:
+    ensembl_gtf: gtf
+    star_index: star
+    """
+    translations = {}
+
+    if "REFGENIE" in os.environ:
+        refgenie_genomes_config_path = os.environ.get("REFGENIE")
+        refgenie_genomes_config_directory = Path(refgenie_genomes_config_path).parents[0]
+    elif "genome_folder" in rgc:
+        refgenie_genomes_config_directory = Path(rgc["genome_folder"])
+    else:
+        return translations
+
+    try:
+        with open(refgenie_genomes_config_directory / "alias_translations.yaml") as yaml_file:
+            translations = yaml.load(yaml_file, Loader=yaml.Loader)
+    except FileNotFoundError:
+        pass
+
+    return translations
+
+
 def update_config(rgc):
     """
     Update the genomes.config file after a local refgenie database has been updated

tests/test_refgenie.py

@@ -7,6 +7,8 @@
 import tempfile
 import unittest
 
+import yaml
+
 
 class TestRefgenie(unittest.TestCase):
     """Class for refgenie tests"""
@@ -19,6 +21,7 @@ def setUp(self):
         self.NXF_HOME = os.path.join(self.tmp_dir, ".nextflow")
         self.NXF_REFGENIE_PATH = os.path.join(self.NXF_HOME, "nf-core", "refgenie_genomes.config")
         self.REFGENIE = os.path.join(self.tmp_dir, "genomes_config.yaml")
+        self.translation_file = os.path.join(self.tmp_dir, "alias_translations.yaml")
         # Set NXF_HOME environment variable
         # avoids adding includeConfig statement to config file outside the current tmpdir
         try:
@@ -37,6 +40,10 @@ def setUp(self):
         with open(self.REFGENIE, "a") as fh:
             fh.write(f"nextflow_config: {os.path.join(self.NXF_REFGENIE_PATH)}\n")
 
+        # Add an alias translation to YAML file
+        with open(self.translation_file, "a") as fh:
+            fh.write("ensembl_gtf: gtf\n")
+
     def tearDown(self) -> None:
         # Remove the tempdir again
         os.system(f"rm -rf {self.tmp_dir}")
@@ -53,3 +60,13 @@ def test_update_refgenie_genomes_config(self):
         out = subprocess.check_output(shlex.split(cmd), stderr=subprocess.STDOUT)
 
         assert "Updated nf-core genomes config" in str(out)
+
+    def test_asset_alias_translation(self):
+        """Test that asset aliases are translated correctly"""
+        # Populate the config with a genome
+        cmd = f"refgenie pull hg38/ensembl_gtf -c {self.REFGENIE}"
+        subprocess.check_output(shlex.split(cmd), stderr=subprocess.STDOUT)
+        cmd = f"cat {self.NXF_REFGENIE_PATH}"
+        out = subprocess.check_output(shlex.split(cmd), stderr=subprocess.STDOUT)
+        assert "      gtf                  = " in str(out)
+        assert "      ensembl_gtf          = " not in str(out)