Add profiles (#36)

* Add case name to output directory path

* Update CHANGELOG

* Bump to rc2

* Fix return type

* Add profiles option

* Update README

* Update CHANGELOG

* Simplify config resolution

* Add quoting for profiles args

CHANGELOG.md

@@ -11,9 +11,10 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ---
 
-## [1.0.0-rc.2] - 2023-02-13
+## [1.0.0-rc.2] - 2023-03-09
 ### Added
 - Case name to output directory path to avoid over-writing
+- Support for Nextflow profiles
 ### Changed
 - Override `skip` from configuration YAML for command line test cases
 

README.md

@@ -140,6 +140,7 @@ The settings available for each case:
 |:--:|:--:|:--:|
 |`temp_dir`|Directory to be added to `NFT_TEMP` environment variable to create Nextflow working directory.|_value from global_|
 |`nf_config`|Path to be added to `NFT_INIT` to derive global `.config` file for Nextflow.|_value from global_|
+|`profiles`|Ordered list of profiles to use with Nextflow through the `-profile` option.|`None`|
 |`remove_temp`|Whether to remove the Nextflow working directory after each case.|_value from global_|
 |`clean_logs`|Whether to remove log files generated by Nextflow.|_value from global_|
 |`name`|Name of the test case; used to identify the case and for selecting specific cases to run.|`None`|

nftest/NFTestCase.py

@@ -3,6 +3,7 @@
 import shutil
 import re
 from pathlib import Path
+from shlex import quote
 import subprocess as sp
 from subprocess import PIPE
 from logging import getLogger
@@ -20,7 +21,7 @@ class NFTestCase():
     # pylint: disable=R0902
     # pylint: disable=R0913
     def __init__(self, name:str=None, message:str=None, nf_script:str=None,
-            nf_configs:List[str]=None, params_file:str=None,
+            nf_configs:List[str]=None, profiles:List[str]=None, params_file:str=None,
             output_directory_param_name:str='output_dir',
             asserts:List[NFTestAssert]=None, temp_dir:str=None,
             remove_temp:bool=None, clean_logs:bool=True,
@@ -33,6 +34,7 @@ def __init__(self, name:str=None, message:str=None, nf_script:str=None,
         self.message = message
         self.nf_script = nf_script
         self.nf_configs = nf_configs or []
+        self.profiles = profiles or []
         self.params_file = params_file
         self.output_directory_param_name = output_directory_param_name
         self.asserts = self.resolve_actual(asserts)
@@ -90,13 +92,15 @@ def submit(self) -> sp.CompletedProcess:
         for nf_config in self.nf_configs:
             config_arg += f'-c {nf_config} '
         params_file_arg = f"-params-file {self.params_file}" if self.params_file else ""
+        profiles_arg = f"-profile {quote(','.join(self.profiles))}" if self.profiles else ""
         output_directory_with_case = Path(self._env.NFT_OUTPUT)/self.name_for_output
         output_directory_arg = f"--{self.output_directory_param_name} " \
             f"{output_directory_with_case}"
         cmd = f"""
         NXF_WORK={self.temp_dir} \
         nextflow run \
             {self.nf_script} \
+            {profiles_arg} \
             {config_arg} \
             {params_file_arg} \
             {output_directory_arg}

nftest/NFTestRunner.py

@@ -32,8 +32,7 @@ def load_from_config(self, config_yaml:str, target_cases:List[str]):
                 else:
                     asserts = []
                 case['asserts'] = asserts
-                case['nf_configs'] = [case['nf_config']] if case['nf_config'] is not None else []
-                del case['nf_config']
+                case['nf_configs'] = [case.pop('nf_config')] if case.get('nf_config', None) else []
                 test_case = NFTestCase(**case)
                 test_case.combine_global(self._global)
                 if target_cases: