Changed module list generation.

libworkflows/__init__.py

 __copyright__ = "Copyright (C) 2020 Blaise Li"
 __licence__ = "GNU GPLv3"
-__version__ = 0.5
+__version__ = 0.6
 from .libworkflows import (
     SHELL_FUNCTIONS, cleanup_and_backup, column_converter,
-    ensure_relative, envmod,
+    ensure_relative, envmods,
     file_len, feature_orientation2stranded, filter_combinator, get_chrom_sizes,
     last_lines, make_id_list_getter,
     partial_format,

libworkflows/libworkflows.py

@@ -23,6 +23,7 @@ from shutil import rmtree
 import warnings
 from collections.abc import Mapping
 from contextlib import contextmanager
+from itertools import chain
 from subprocess import Popen, PIPE
 from re import compile as rcompile, sub
 from textwrap import indent
@@ -218,12 +219,12 @@ def run_with_modules(
     return (real_cmd, generic_shell_commands)
 
 
-def envmod(
+def envmods(
         mod_name,
         module_versions,
         dependency=None):
     """
-    Generate the string representing the module to be loaded.
+    Generate a list of string representing the modules to be loaded.
 
     *mod_name* will be used as a key in the *module_versions*
     dictionary in order to get the associated version number.
@@ -233,9 +234,13 @@ def envmod(
     for module *mod_name* (including *mod_name* itself) where
     *dependency* will be found as a key.
     """
+    if isinstance(module_versions[mod_name], Mapping):
+        return list(chain.from_iterable(
+            envmods(mod_name, module_versions, dependency=dependency)
+            for dependency in module_versions[mod_name]))
     if dependency is None:
-        return f"{mod_name}/{module_versions[mod_name]}"
-    return f"{dependency}/{module_versions[mod_name][dependency]}"
+        return [f"{mod_name}/{module_versions[mod_name]}"]
+    return [f"{dependency}/{module_versions[mod_name][dependency]}"]
 
 
 def run_and_write_methods(
@@ -265,17 +270,12 @@ def run_and_write_methods(
         try:
             # Only one module, whose dependencies
             # are assumed to be defined as a sub-dictionary of module_versions
-            [main_module] = params.modules
-            if isinstance(module_versions[main_module], Mapping):
-                modules = [
-                    envmod(main_module, module_versions, dependency=module)
-                    for module in module_versions[main_module]]
-            else:
-                modules = [envmod(main_module, module_versions)]
+            [mod_name] = params.modules
+            modules = envmods(mod_name, module_versions)
         except ValueError:
-            modules = [
-                envmod(module, module_versions)
-                for module in params.modules]
+            modules = list(chain.from_iterable(
+                envmods(mod_name, module_versions)
+                for mod_name in params.modules))
         cmd = run_with_modules(
             cmd,
             generic_shell_commands=generic_cmd,