From 297735e06df52450a6a133dade10ad45a3f1799e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 10:46:34 +0200 Subject: [PATCH 01/12] add --fix option to fix the meta.yml of subworkflows --- nf_core/__main__.py | 5 +- nf_core/commands_subworkflows.py | 3 +- nf_core/components/nfcore_component.py | 142 +++++++++++++++---------- nf_core/subworkflows/lint/__init__.py | 55 +++++++++- nf_core/subworkflows/lint/meta_yml.py | 6 ++ tests/subworkflows/lint.py | 9 ++ tests/test_subworkflows.py | 1 + 7 files changed, 162 insertions(+), 59 deletions(-) diff --git a/nf_core/__main__.py b/nf_core/__main__.py index 1dd92d6b8f..dd800ad810 100644 --- a/nf_core/__main__.py +++ b/nf_core/__main__.py @@ -1431,11 +1431,12 @@ def command_subworkflows_list_local(ctx, keywords, json, dir): # pylint: disabl help="Sort lint output by subworkflow or test name.", show_default=True, ) -def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +@click.option("--fix", is_flag=True, help="Fix all linting tests if possible.") +def command_subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix): """ Lint one or more subworkflows in a directory. """ - subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by) + subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix) # nf-core subworkflows info diff --git a/nf_core/commands_subworkflows.py b/nf_core/commands_subworkflows.py index cc1a544eca..70a0c94edc 100644 --- a/nf_core/commands_subworkflows.py +++ b/nf_core/commands_subworkflows.py @@ -102,7 +102,7 @@ def subworkflows_list_local(ctx, keywords, json, dir): # pylint: disable=redefi sys.exit(1) -def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by): +def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, local, passed, sort_by, fix): """ Lint one or more subworkflows in a directory. @@ -119,6 +119,7 @@ def subworkflows_lint(ctx, subworkflow, dir, registry, key, all, fail_warned, lo subworkflow_lint = SubworkflowLint( dir, fail_warned=fail_warned, + fix=fix, registry=ctx.params["registry"], remote_url=ctx.obj["modules_repo_url"], branch=ctx.obj["modules_repo_branch"], diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index 3e5a68648d..db817db905 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -41,6 +41,7 @@ def __init__( remote_component (bool): Whether the module is to be treated as a nf-core or local component """ + self.component_type = component_type self.component_name = component_name self.repo_url = repo_url self.component_dir = component_dir @@ -155,67 +156,98 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st included_components.append(component) return included_components - def get_inputs_from_main_nf(self): + def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" inputs = [] with open(self.main_nf) as f: data = f.read() - # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo - # regex matches: - # val(foo) - # path(bar) - # val foo - # val bar - # path bar - # path foo - # don't match anything inside comments or after "output:" - if "input:" not in data: - log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs - input_data = data.split("input:")[1].split("output:")[0] - for line in input_data.split("\n"): - channel_elements = [] - regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" - matches = re.finditer(regex, line) - for _, match in enumerate(matches, start=1): - input_val = None - if match.group(3): - input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - elif match.group(4): - input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases - if input_val: - channel_elements.append({input_val: {}}) - if len(channel_elements) > 0: - inputs.append(channel_elements) - log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") - self.inputs = inputs + if self.component_type == "modules": + # get input values from main.nf after "input:", which can be formatted as tuple val(foo) path(bar) or val foo or val bar or path bar or path foo + # regex matches: + # val(foo) + # path(bar) + # val foo + # val bar + # path bar + # path foo + # don't match anything inside comments or after "output:" + if "input:" not in data: + log.debug(f"Could not find any inputs in {self.main_nf}") + return inputs + input_data = data.split("input:")[1].split("output:")[0] + for line in input_data.split("\n"): + channel_elements = [] + regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + matches = re.finditer(regex, line) + for _, match in enumerate(matches, start=1): + input_val = None + if match.group(3): + input_val = match.group(3).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + elif match.group(4): + input_val = match.group(4).split(",")[0] # handle `files, stageAs: "inputs/*"` cases + if input_val: + channel_elements.append({input_val: {}}) + if len(channel_elements) > 0: + inputs.append(channel_elements) + log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") + self.inputs = inputs + elif self.component_type == "subworkflows": + # get input values from main.nf after "take:" + if "take:" not in data: + log.debug(f"Could not find any inputs in {self.main_nf}") + return inputs + # get all lines between "take" and "main" or "emit" + input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0] + for line in input_data.split("\n"): + try: + inputs.append(line.split()[0]) + except IndexError: + # Empty lines + pass + log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") + self.inputs = inputs def get_outputs_from_main_nf(self): outputs = [] with open(self.main_nf) as f: data = f.read() - # get output values from main.nf after "output:". the names are always after "emit:" - if "output:" not in data: - log.debug(f"Could not find any outputs in {self.main_nf}") - return outputs - output_data = data.split("output:")[1].split("when:")[0] - regex_emit = r"emit:\s*([^)\s,]+)" - regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))" - for line in output_data.split("\n"): - match_emit = re.search(regex_emit, line) - matches_elements = re.finditer(regex_elements, line) - if not match_emit: - continue - output_channel = {match_emit.group(1): []} - for _, match_element in enumerate(matches_elements, start=1): - output_val = None - if match_element.group(3): - output_val = match_element.group(3) - elif match_element.group(4): - output_val = match_element.group(4) - if output_val: - output_val = output_val.strip("'").strip('"') # remove quotes - output_channel[match_emit.group(1)].append({output_val: {}}) - outputs.append(output_channel) - log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") - self.outputs = outputs + if self.component_type == "modules": + # get output values from main.nf after "output:". the names are always after "emit:" + if "output:" not in data: + log.debug(f"Could not find any outputs in {self.main_nf}") + return outputs + output_data = data.split("output:")[1].split("when:")[0] + regex_emit = r"emit:\s*([^)\s,]+)" + regex_elements = r"(val|path|env|stdout)\s*(\(([^)]+)\)|\s*([^)\s,]+))" + for line in output_data.split("\n"): + match_emit = re.search(regex_emit, line) + matches_elements = re.finditer(regex_elements, line) + if not match_emit: + continue + output_channel = {match_emit.group(1): []} + for _, match_element in enumerate(matches_elements, start=1): + output_val = None + if match_element.group(3): + output_val = match_element.group(3) + elif match_element.group(4): + output_val = match_element.group(4) + if output_val: + output_val = output_val.strip("'").strip('"') # remove quotes + output_channel[match_emit.group(1)].append({output_val: {}}) + outputs.append(output_channel) + log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") + self.outputs = outputs + elif self.component_type == "subworkflows": + # get output values from main.nf after "emit:". Can be named outputs or not. + if "emit:" not in data: + log.debug(f"Could not find any outputs in {self.main_nf}") + return outputs + output_data = data.split("emit:")[1].split("}")[0] + for line in output_data.split("\n"): + try: + outputs.append(line.split("=")[0].split()[0]) + except IndexError: + # Empty lines + pass + log.debug(f"Found {len(outputs)} outputs in {self.main_nf}") + self.outputs = outputs diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index a3cacf2952..e0911e5bd9 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -11,11 +11,12 @@ import questionary import rich +import ruamel.yaml import nf_core.modules.modules_utils import nf_core.utils from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult -from nf_core.pipelines.lint_utils import console +from nf_core.pipelines.lint_utils import console, run_prettier_on_file log = logging.getLogger(__name__) @@ -38,6 +39,7 @@ def __init__( self, dir, fail_warned=False, + fix=False, remote_url=None, branch=None, no_pull=False, @@ -48,6 +50,7 @@ def __init__( component_type="subworkflows", dir=dir, fail_warned=fail_warned, + fix=fix, remote_url=remote_url, branch=branch, no_pull=no_pull, @@ -207,6 +210,10 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): # Otherwise run all the lint tests else: + # Update meta.yml file if requested + if self.fix: + self.update_meta_yml_file(swf) + if self.repo_type == "pipeline" and self.modules_json: # Set correct sha version = self.modules_json.get_subworkflow_version(swf.component_name, swf.repo_url, swf.org) @@ -223,3 +230,49 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): self.failed += warned self.failed += [LintResult(swf, *s) for s in swf.failed] + + + def update_meta_yml_file(self, swf): + """ + Update the meta.yml file with the correct inputs and outputs + """ + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + yaml.indent(mapping=2, sequence=2, offset=0) + + # Read meta.yml + with open(swf.meta_yml) as fh: + meta_yaml = yaml.load(fh) + meta_yaml_corrected = meta_yaml.copy() + # Obtain inputs and outputs from main.nf + swf.get_inputs_from_main_nf() + swf.get_outputs_from_main_nf() + + # Compare inputs and add them if missing + if "input" in meta_yaml: + # Delete inputs from meta.yml which are not present in main.nf + meta_yaml_corrected["input"] = [input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs] + # Obtain inputs from main.nf missing in meta.yml + inputs_correct = [list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs] + inputs_missing = [input for input in swf.inputs if input not in inputs_correct] + # Add missing inputs to meta.yml + for missing_input in inputs_missing: + meta_yaml_corrected["input"].append({missing_input: {"description": ""}}) + + if "output" in meta_yaml: + # Delete outputs from meta.yml which are not present in main.nf + meta_yaml_corrected["output"] = [output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs] + # Obtain output from main.nf missing in meta.yml + outputs_correct = [list(output.keys())[0] for output in meta_yaml_corrected["output"] if list(output.keys())[0] in swf.outputs] + outputs_missing = [output for output in swf.outputs if output not in outputs_correct] + # Add missing inputs to meta.yml + for missing_output in outputs_missing: + meta_yaml_corrected["output"].append({missing_output: {"description": ""}}) + + # Write corrected meta.yml to file + with open(swf.meta_yml, "w") as fh: + log.info(f"Updating {swf.meta_yml}") + yaml.dump(meta_yaml_corrected, fh) + run_prettier_on_file(fh.name) + + diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py index 24e75eddbf..633061e247 100644 --- a/nf_core/subworkflows/lint/meta_yml.py +++ b/nf_core/subworkflows/lint/meta_yml.py @@ -1,4 +1,5 @@ import json +import logging from pathlib import Path import jsonschema.validators @@ -6,6 +7,7 @@ import nf_core.components.components_utils +log = logging.getLogger(__name__) def meta_yml(subworkflow_lint_object, subworkflow): """ @@ -65,6 +67,8 @@ def meta_yml(subworkflow_lint_object, subworkflow): subworkflow.passed.append(("meta_input", f"`{input}` specified", subworkflow.meta_yml)) else: subworkflow.failed.append(("meta_input", f"`{input}` missing in `meta.yml`", subworkflow.meta_yml)) + else: + log.debug(f"No inputs specified in subworkflow `main.nf`: {subworkflow.component_name}") if "output" in meta_yaml: meta_output = [list(x.keys())[0] for x in meta_yaml["output"]] @@ -75,6 +79,8 @@ def meta_yml(subworkflow_lint_object, subworkflow): subworkflow.failed.append( ("meta_output", f"`{output}` missing in `meta.yml`", subworkflow.meta_yml) ) + else: + log.debug(f"No outputs specified in subworkflow `main.nf`: {subworkflow.component_name}") # confirm that the name matches the process name in main.nf if meta_yaml["name"].upper() == subworkflow.workflow_name: diff --git a/tests/subworkflows/lint.py b/tests/subworkflows/lint.py index 540f421ad2..35e2c6b519 100644 --- a/tests/subworkflows/lint.py +++ b/tests/subworkflows/lint.py @@ -38,6 +38,15 @@ def test_subworkflows_lint_new_subworkflow(self): assert len(subworkflow_lint.warned) >= 0 +def test_subworkflows_lint_update_meta_yml(self): + """update the meta.yml of a subworkflow""" + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules, fix=True) + subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") + assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" + assert len(subworkflow_lint.passed) > 0 + assert len(subworkflow_lint.warned) >= 0 + + def test_subworkflows_lint_no_gitlab(self): """Test linting a pipeline with no subworkflows installed""" with pytest.raises(LookupError): diff --git a/tests/test_subworkflows.py b/tests/test_subworkflows.py index 786ba53836..cb8bcf7a56 100644 --- a/tests/test_subworkflows.py +++ b/tests/test_subworkflows.py @@ -159,6 +159,7 @@ def tearDown(self): test_subworkflows_lint_snapshot_file, test_subworkflows_lint_snapshot_file_missing_fail, test_subworkflows_lint_snapshot_file_not_needed, + test_subworkflows_lint_update_meta_yml, ) from .subworkflows.list import ( # type: ignore[misc] test_subworkflows_install_and_list_subworkflows, From a79a4f0e0c4ad3546c39d22ef46ce74e9bc25de8 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 12:12:17 +0200 Subject: [PATCH 02/12] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 16db104fc6..e25e8f8948 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ ### Components - The `modules_nfcore` tag in the `main.nf.test` file of modules/subworkflows now displays the organization name in custom modules repositories ([#3005](https://github.com/nf-core/tools/pull/3005)) +- Add option `--fix` to update the `meta.yml` file of subworkflows ([#3077](https://github.com/nf-core/tools/pull/3077)) ### General From 2d2be3877fe04dbc4ddb80cf525be0db13083740 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Wed, 24 Jul 2024 16:03:33 +0200 Subject: [PATCH 03/12] fix typing and linting --- nf_core/components/nfcore_component.py | 11 +++++------ nf_core/subworkflows/lint/__init__.py | 21 ++++++++++++++------- nf_core/subworkflows/lint/meta_yml.py | 1 + 3 files changed, 20 insertions(+), 13 deletions(-) diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py index db817db905..39a4ba51f4 100644 --- a/nf_core/components/nfcore_component.py +++ b/nf_core/components/nfcore_component.py @@ -158,7 +158,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st def get_inputs_from_main_nf(self) -> None: """Collect all inputs from the main.nf file.""" - inputs = [] + inputs: list[list | str] = [] with open(self.main_nf) as f: data = f.read() if self.component_type == "modules": @@ -173,10 +173,10 @@ def get_inputs_from_main_nf(self) -> None: # don't match anything inside comments or after "output:" if "input:" not in data: log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs + return input_data = data.split("input:")[1].split("output:")[0] for line in input_data.split("\n"): - channel_elements = [] + channel_elements: list[dict] = [] regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))" matches = re.finditer(regex, line) for _, match in enumerate(matches, start=1): @@ -195,15 +195,14 @@ def get_inputs_from_main_nf(self) -> None: # get input values from main.nf after "take:" if "take:" not in data: log.debug(f"Could not find any inputs in {self.main_nf}") - return inputs + return # get all lines between "take" and "main" or "emit" input_data = data.split("take:")[1].split("main:")[0].split("emit:")[0] for line in input_data.split("\n"): try: inputs.append(line.split()[0]) except IndexError: - # Empty lines - pass + pass # Empty lines log.debug(f"Found {len(inputs)} inputs in {self.main_nf}") self.inputs = inputs diff --git a/nf_core/subworkflows/lint/__init__.py b/nf_core/subworkflows/lint/__init__.py index e0911e5bd9..22025d2a07 100644 --- a/nf_core/subworkflows/lint/__init__.py +++ b/nf_core/subworkflows/lint/__init__.py @@ -231,7 +231,6 @@ def lint_subworkflow(self, swf, progress_bar, registry, local=False): self.failed += [LintResult(swf, *s) for s in swf.failed] - def update_meta_yml_file(self, swf): """ Update the meta.yml file with the correct inputs and outputs @@ -251,9 +250,13 @@ def update_meta_yml_file(self, swf): # Compare inputs and add them if missing if "input" in meta_yaml: # Delete inputs from meta.yml which are not present in main.nf - meta_yaml_corrected["input"] = [input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs] + meta_yaml_corrected["input"] = [ + input for input in meta_yaml["input"] if list(input.keys())[0] in swf.inputs + ] # Obtain inputs from main.nf missing in meta.yml - inputs_correct = [list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs] + inputs_correct = [ + list(input.keys())[0] for input in meta_yaml_corrected["input"] if list(input.keys())[0] in swf.inputs + ] inputs_missing = [input for input in swf.inputs if input not in inputs_correct] # Add missing inputs to meta.yml for missing_input in inputs_missing: @@ -261,9 +264,15 @@ def update_meta_yml_file(self, swf): if "output" in meta_yaml: # Delete outputs from meta.yml which are not present in main.nf - meta_yaml_corrected["output"] = [output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs] + meta_yaml_corrected["output"] = [ + output for output in meta_yaml["output"] if list(output.keys())[0] in swf.outputs + ] # Obtain output from main.nf missing in meta.yml - outputs_correct = [list(output.keys())[0] for output in meta_yaml_corrected["output"] if list(output.keys())[0] in swf.outputs] + outputs_correct = [ + list(output.keys())[0] + for output in meta_yaml_corrected["output"] + if list(output.keys())[0] in swf.outputs + ] outputs_missing = [output for output in swf.outputs if output not in outputs_correct] # Add missing inputs to meta.yml for missing_output in outputs_missing: @@ -274,5 +283,3 @@ def update_meta_yml_file(self, swf): log.info(f"Updating {swf.meta_yml}") yaml.dump(meta_yaml_corrected, fh) run_prettier_on_file(fh.name) - - diff --git a/nf_core/subworkflows/lint/meta_yml.py b/nf_core/subworkflows/lint/meta_yml.py index 633061e247..be282bc453 100644 --- a/nf_core/subworkflows/lint/meta_yml.py +++ b/nf_core/subworkflows/lint/meta_yml.py @@ -9,6 +9,7 @@ log = logging.getLogger(__name__) + def meta_yml(subworkflow_lint_object, subworkflow): """ Lint a ``meta.yml`` file From ebfbd9884f9c6dddfbf18feeb5945ce659c7c43d Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 20 Sep 2024 18:16:40 +0200 Subject: [PATCH 04/12] fix pytests by mocking biotools, adding a meta to the test module and running prettier to meta.yml file --- tests/test_modules.py | 15 +++++++++++---- tests/utils.py | 9 +++++++++ 2 files changed, 20 insertions(+), 4 deletions(-) diff --git a/tests/test_modules.py b/tests/test_modules.py index 0e16497176..d0692236e8 100644 --- a/tests/test_modules.py +++ b/tests/test_modules.py @@ -7,7 +7,7 @@ import pytest import requests_cache import responses -import yaml +import ruamel.yaml import nf_core.modules import nf_core.modules.create @@ -16,6 +16,7 @@ import nf_core.modules.remove import nf_core.pipelines.create.create from nf_core import __version__ +from nf_core.pipelines.lint_utils import run_prettier_on_file from nf_core.utils import NFCoreYamlConfig from .utils import ( @@ -28,11 +29,15 @@ create_tmp_pipeline, mock_anaconda_api_calls, mock_biocontainers_api_calls, + mock_biotools_api_calls, ) def create_modules_repo_dummy(tmp_dir): """Create a dummy copy of the nf-core/modules repo""" + yaml = ruamel.yaml.YAML() + yaml.preserve_quotes = True + yaml.indent(mapping=2, sequence=2, offset=0) root_dir = Path(tmp_dir, "modules") Path(root_dir, "modules", "nf-core").mkdir(parents=True) @@ -42,13 +47,14 @@ def create_modules_repo_dummy(tmp_dir): nf_core_yml = NFCoreYamlConfig(nf_core_version=__version__, repository_type="modules", org_path="nf-core") with open(Path(root_dir, ".nf-core.yml"), "w") as fh: yaml.dump(nf_core_yml.model_dump(), fh) - # mock biocontainers and anaconda response + # mock biocontainers and anaconda response and biotools response with responses.RequestsMock() as rsps: mock_anaconda_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") mock_biocontainers_api_calls(rsps, "bpipe", "0.9.13--hdfd78af_0") + mock_biotools_api_calls(rsps, "bpipe") # bpipe is a valid package on bioconda that is very unlikely to ever be added to nf-core/modules module_create = nf_core.modules.create.ModuleCreate( - root_dir, "bpipe/test", "@author", "process_single", False, False + root_dir, "bpipe/test", "@author", "process_single", True, False ) with requests_cache.disabled(): assert module_create.create() @@ -57,10 +63,11 @@ def create_modules_repo_dummy(tmp_dir): meta_yml_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "meta.yml") with open(str(meta_yml_path)) as fh: - meta_yml = yaml.safe_load(fh) + meta_yml = yaml.load(fh) del meta_yml["tools"][0]["bpipe"]["doi"] with open(str(meta_yml_path), "w") as fh: yaml.dump(meta_yml, fh) + run_prettier_on_file(fh.name) # Add dummy content to main.nf.test.snap test_snap_path = Path(root_dir, "modules", "nf-core", "bpipe", "test", "tests", "main.nf.test.snap") diff --git a/tests/utils.py b/tests/utils.py index 1d5a8a115d..6f4b73cccc 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -98,6 +98,15 @@ def mock_biocontainers_api_calls(rsps: responses.RequestsMock, module: str, vers rsps.get(biocontainers_api_url, json=biocontainers_mock, status=200) +def mock_biotools_api_calls(rsps: responses.RequestsMock, module: str) -> None: + """Mock biotools api calls for module""" + biotools_api_url = f"https://bio.tools/api/t/?q={module}&format=json" + biotools_mock = { + "list": [{"name": "Bpipe", "biotoolsCURIE": "biotools:bpipe"}], + } + rsps.get(biotools_api_url, json=biotools_mock, status=200) + + def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: """Create a new Pipeline for testing""" From 0447d1a28a802922bd3e9fa9f184ed9f3eb0b8da Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 12:52:22 +0200 Subject: [PATCH 05/12] update template modules --- nf_core/pipeline-template/modules.json | 4 +- .../modules/nf-core/fastqc/main.nf | 5 +- .../modules/nf-core/fastqc/meta.yml | 57 ++++++++------ .../modules/nf-core/multiqc/environment.yml | 3 +- .../modules/nf-core/multiqc/main.nf | 14 +++- .../modules/nf-core/multiqc/meta.yml | 78 ++++++++++++------- 6 files changed, 100 insertions(+), 61 deletions(-) diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 367202155a..9bc344e7d1 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -8,12 +8,12 @@ {%- if fastqc %} "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } {%- endif %} diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf index d79f1c862d..d8989f4812 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf @@ -26,7 +26,10 @@ process FASTQC { def rename_to = old_new_pairs*.join(' ').join(' ') def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') + // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) + // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 + // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label + def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') / task.cpus // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml index ee5507e06b..4827da7af2 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml index 329ddb4870..f1cd99b079 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml @@ -1,6 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.24.1 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 47ac352f94..b9ccebdbbc 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -23,16 +25,22 @@ process MULTIQC { script: def args = task.ext.args ?: '' + def prefix = task.ext.prefix ? "--filename ${task.ext.prefix}.html" : '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ $args \\ $config \\ + $prefix \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml index 45a9bc35e1..b16c187923 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,40 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" From 200ae85466eef6f544227bf9556be686c2161946 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 12:53:06 +0200 Subject: [PATCH 06/12] add testing the module name back --- nf_core/modules/lint/meta_yml.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py index 4f7ffd0739..4ad728d10b 100644 --- a/nf_core/modules/lint/meta_yml.py +++ b/nf_core/modules/lint/meta_yml.py @@ -95,6 +95,23 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None # Confirm that all input and output channels are correctly specified if valid_meta_yml: + # confirm that the name matches the process name in main.nf + if meta_yaml["name"].upper() == module.process_name: + module.passed.append( + ( + "meta_name", + "Correct name specified in `meta.yml`.", + module.meta_yml, + ) + ) + else: + module.failed.append( + ( + "meta_name", + f"Conflicting `process` name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)", + module.meta_yml, + ) + ) # Check that inputs are specified in meta.yml if len(module.inputs) > 0 and "input" not in meta_yaml: module.failed.append( From 0e3a35b64aa814911e9eb61ee7c23cee51413cbc Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 12:53:42 +0200 Subject: [PATCH 07/12] fix info command for the new yaml structure --- nf_core/components/info.py | 53 ++++++++++++++++++++++++++++---------- 1 file changed, 39 insertions(+), 14 deletions(-) diff --git a/nf_core/components/info.py b/nf_core/components/info.py index 98f8be5272..e4a58d1618 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -280,14 +280,26 @@ def generate_component_info_help(self): inputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) inputs_table.add_column(":inbox_tray: Inputs") inputs_table.add_column("Description") - inputs_table.add_column("Pattern", justify="right", style="green") + if self.component_type == "modules": + inputs_table.add_column("Pattern", justify="right", style="green") + elif self.component_type == "subworkflows": + inputs_table.add_column("Structure", justify="right", style="green") for input in self.meta["input"]: - for key, info in input.items(): - inputs_table.add_row( - f"[orange1 on black] {key} [/][dim i] ({info['type']})", - Markdown(info["description"] if info["description"] else ""), - info.get("pattern", ""), - ) + if self.component_type == "modules": + for element in input: + for key, info in element.items(): + inputs_table.add_row( + f"[orange1 on black] {key} [/][dim i] ({info['type']})", + Markdown(info["description"] if info["description"] else ""), + info.get("pattern", ""), + ) + elif self.component_type == "subworkflows": + for key, info in input.items(): + inputs_table.add_row( + f"[orange1 on black] {key} [/][dim i]", + Markdown(info["description"] if info["description"] else ""), + info.get("structure", ""), + ) renderables.append(inputs_table) @@ -296,14 +308,27 @@ def generate_component_info_help(self): outputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) outputs_table.add_column(":outbox_tray: Outputs") outputs_table.add_column("Description") - outputs_table.add_column("Pattern", justify="right", style="green") + if self.component_type == "modules": + inputs_table.add_column("Pattern", justify="right", style="green") + elif self.component_type == "subworkflows": + inputs_table.add_column("Structure", justify="right", style="green") for output in self.meta["output"]: - for key, info in output.items(): - outputs_table.add_row( - f"[orange1 on black] {key} [/][dim i] ({info['type']})", - Markdown(info["description"] if info["description"] else ""), - info.get("pattern", ""), - ) + if self.component_type == "modules": + for ch_name, elements in output.items(): + for element in elements: + for key, info in element.items(): + outputs_table.add_row( + f"[orange1 on black] {key} [/][dim i] ({info['type']})", + Markdown(info["description"] if info["description"] else ""), + info.get("pattern", ""), + ) + elif self.component_type == "subworkflows": + for key, info in output.items(): + outputs_table.add_row( + f"[orange1 on black] {key} [/][dim i]", + Markdown(info["description"] if info["description"] else ""), + info.get("structure", ""), + ) renderables.append(outputs_table) From 23c2612c561dd4489c17df1f0f4b3c95d091e8e5 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 12:54:32 +0200 Subject: [PATCH 08/12] fix modules pytest --- nf_core/module-template/meta.yml | 10 +++---- tests/modules/test_lint.py | 45 ++++++++------------------------ tests/modules/test_patch.py | 4 +-- 3 files changed, 18 insertions(+), 41 deletions(-) diff --git a/nf_core/module-template/meta.yml b/nf_core/module-template/meta.yml index c7c16dcb38..d9d1cc8ae8 100644 --- a/nf_core/module-template/meta.yml +++ b/nf_core/module-template/meta.yml @@ -53,11 +53,6 @@ input: ## TODO nf-core: Add a description of all of the variables used as output {% endif -%} output: - - versions: - - "versions.yml": - type: file - description: File containing software versions - pattern: "versions.yml" - {{ 'bam:' if not_empty_template else "output:" }} #{% if has_meta -%} Only when we have meta - meta: @@ -81,6 +76,11 @@ output: {% else -%} - edam: "" {%- endif %} + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "{{ author }}" diff --git a/tests/modules/test_lint.py b/tests/modules/test_lint.py index f4adedfcb5..5372807987 100644 --- a/tests/modules/test_lint.py +++ b/tests/modules/test_lint.py @@ -210,14 +210,6 @@ def test_modules_lint_new_modules(self): assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 - def test_modules_lint_update_meta_yml(self): - """update the meta.yml of a module""" - module_lint = nf_core.modules.ModuleLint(directory=self.nfcore_modules, fix=True) - module_lint.lint(print_results=False, module="fastqc") - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) > 0 - assert len(module_lint.warned) >= 0 - def test_modules_lint_no_gitlab(self): """Test linting a pipeline with no modules installed""" self.mods_remove.remove("fastqc", force=True) @@ -282,7 +274,7 @@ def test_modules_lint_patched_modules(self): all_modules=True, ) - assert len(module_lint.failed) == 1 + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) > 0 assert len(module_lint.warned) >= 0 @@ -313,6 +305,14 @@ def test_modules_lint_check_url(self): len(mocked_ModuleLint.failed) == failed ), f"{test}: Expected {failed} FAIL, got {len(mocked_ModuleLint.failed)}." + def test_modules_lint_update_meta_yml(self): + """update the meta.yml of a module""" + module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules, fix=True) + module_lint.lint(print_results=False, module="bpipe/test") + assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.passed) > 0 + assert len(module_lint.warned) >= 0 + def test_modules_lint_snapshot_file(self): """Test linting a module with a snapshot file""" module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) @@ -521,25 +521,6 @@ def test_modules_meta_yml_incorrect_licence_field(self): assert len(module_lint.warned) >= 0 assert module_lint.failed[0].lint_test == "meta_yml_valid" - def test_modules_meta_yml_input_mismatch(self): - """Test linting a module with an extra entry in input fields in meta.yml compared to module.input""" - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: - main_nf = fh.read() - main_nf_new = main_nf.replace("path bam", "path bai") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf_new) - module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules) - module_lint.lint(print_results=False, module="bpipe/test") - with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: - fh.write(main_nf) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" - assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2, f"Linting warning with {[x.__dict__ for x in module_lint.warned]}" - lint_tests = [x.lint_test for x in module_lint.warned] - # check that it is there twice: - assert lint_tests.count("meta_input_meta_only") == 1 - assert lint_tests.count("meta_input_main_only") == 1 - def test_modules_meta_yml_output_mismatch(self): """Test linting a module with an extra entry in output fields in meta.yml compared to module.output""" with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf")) as fh: @@ -551,13 +532,9 @@ def test_modules_meta_yml_output_mismatch(self): module_lint.lint(print_results=False, module="bpipe/test") with open(Path(self.nfcore_modules, "modules", "nf-core", "bpipe", "test", "main.nf"), "w") as fh: fh.write(main_nf) - assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" + assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}" assert len(module_lint.passed) >= 0 - assert len(module_lint.warned) == 2 - lint_tests = [x.lint_test for x in module_lint.warned] - # check that it is there twice: - assert lint_tests.count("meta_output_meta_only") == 1 - assert lint_tests.count("meta_output_main_only") == 1 + assert "Module `meta.yml` does not match `main.nf`" in module_lint.failed[0].message def test_modules_meta_yml_incorrect_name(self): """Test linting a module with an incorrect name in meta.yml""" diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py index c3eb94d374..1cdb400ef1 100644 --- a/tests/modules/test_patch.py +++ b/tests/modules/test_patch.py @@ -21,8 +21,8 @@ testing if the update commands works correctly with patch files """ -ORG_SHA = "002623ccc88a3b0cb302c7d8f13792a95354d9f2" -CORRECT_SHA = "1dff30bfca2d98eb7ac7b09269a15e822451d99f" +ORG_SHA = "63e780200600e340365b669f9c673b670764c569" +CORRECT_SHA = "63e780200600e340365b669f9c673b670764c569" SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e" FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73" BISMARK_ALIGN = "bismark/align" From b41e64c2e664db3c3464bf19dd75d99ec67228cb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 13:41:48 +0200 Subject: [PATCH 09/12] fix subworkflows pytest --- tests/subworkflows/test_lint.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py index 1598531d2d..d94b55b3d3 100644 --- a/tests/subworkflows/test_lint.py +++ b/tests/subworkflows/test_lint.py @@ -65,7 +65,7 @@ def test_subworkflows_lint_multiple_remotes(self): def test_subworkflows_lint_update_meta_yml(self): """update the meta.yml of a subworkflow""" - subworkflow_lint = nf_core.subworkflows.SubworkflowLint(dir=self.nfcore_modules, fix=True) + subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.nfcore_modules, fix=True) subworkflow_lint.lint(print_results=False, subworkflow="test_subworkflow") assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}" assert len(subworkflow_lint.passed) > 0 From b249b135ed5810fbdc29f6013e297cc2820f9234 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 14:02:41 +0200 Subject: [PATCH 10/12] update pipeline for multiqc update --- nf_core/pipeline-template/workflows/pipeline.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 5b7e0ff143..f878bb31a2 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -95,7 +95,9 @@ workflow {{ short_name|upper }} { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [] ) {% endif %} emit: From a2ffa4427e7feb877c2fe1fe4e0f7ebf82463893 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 23 Sep 2024 15:10:02 +0200 Subject: [PATCH 11/12] fix more pytests --- .../modules/nf-core/fastqc/tests/main.nf.test | 225 ++++++++--- .../nf-core/fastqc/tests/main.nf.test.snap | 370 ++++++++++++++++-- .../nf-core/multiqc/tests/main.nf.test | 8 + .../nf-core/multiqc/tests/main.nf.test.snap | 20 +- tests/modules/test_patch.py | 26 +- 5 files changed, 529 insertions(+), 120 deletions(-) diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test index 70edae4d99..e9d79a074e 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c31154..d5db3092fb 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test index f1c4242ef2..33316a7ddb 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { tag "modules_nfcore" tag "multiqc" + config "./nextflow.config" + test("sarscov2 single-end [fastqc]") { when { @@ -17,6 +19,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +45,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +72,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap index bfebd80298..b779e46924 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} \ No newline at end of file +} diff --git a/tests/modules/test_patch.py b/tests/modules/test_patch.py index 1cdb400ef1..2f60cd4a20 100644 --- a/tests/modules/test_patch.py +++ b/tests/modules/test_patch.py @@ -21,10 +21,10 @@ testing if the update commands works correctly with patch files """ -ORG_SHA = "63e780200600e340365b669f9c673b670764c569" +ORG_SHA = "3dc7c14d29af40f1a0871a675364e437559d97a8" CORRECT_SHA = "63e780200600e340365b669f9c673b670764c569" -SUCCEED_SHA = "ba15c20c032c549d77c5773659f19c2927daf48e" -FAIL_SHA = "67b642d4471c4005220a342cad3818d5ba2b5a73" +SUCCEED_SHA = "0d0515c3f11266e1314e129bec3e308f804c8dc7" +FAIL_SHA = "cb64a5c1ef85619b89ab99dec2e9097fe84e1dc8" BISMARK_ALIGN = "bismark/align" REPO_NAME = "nf-core-test" PATCH_BRANCH = "patch-tester" @@ -76,7 +76,7 @@ def test_create_patch_no_change(self): module_path = Path(self.pipeline_dir, "modules", REPO_NAME, BISMARK_ALIGN) # Check that no patch file has been added to the directory - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml"} # Check the 'modules.json' contains no patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -94,7 +94,7 @@ def test_create_patch_change(self): patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -127,7 +127,7 @@ def test_create_patch_try_apply_successful(self): patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -153,7 +153,7 @@ def test_create_patch_try_apply_successful(self): update_obj.move_files_from_tmp_dir(BISMARK_ALIGN, install_dir, REPO_NAME, SUCCEED_SHA) # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -195,7 +195,7 @@ def test_create_patch_try_apply_failed(self): patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -234,7 +234,7 @@ def test_create_patch_update_success(self): patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -254,7 +254,7 @@ def test_create_patch_update_success(self): assert update_obj.update(BISMARK_ALIGN) # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -295,7 +295,7 @@ def test_create_patch_update_fail(self): patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" # Check that a patch file with the correct name has been created - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -349,7 +349,7 @@ def test_remove_patch(self): # Check that a patch file with the correct name has been created patch_fn = f"{'-'.join(BISMARK_ALIGN.split('/'))}.diff" - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", patch_fn} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml", patch_fn} # Check the 'modules.json' contains a patch file for the module modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) @@ -361,7 +361,7 @@ def test_remove_patch(self): mock_questionary.unsafe_ask.return_value = True patch_obj.remove(BISMARK_ALIGN) # Check that the diff file has been removed - assert set(os.listdir(module_path)) == {"main.nf", "meta.yml"} + assert set(os.listdir(module_path)) == {"main.nf", "meta.yml", "environment.yml"} # Check that the 'modules.json' entry has been removed modules_json_obj = nf_core.modules.modules_json.ModulesJson(self.pipeline_dir) From 8d5f898f3114d1b029963af7ed60590b56288175 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 27 Sep 2024 11:51:12 +0200 Subject: [PATCH 12/12] remove code duplication and format components info command --- nf_core/components/info.py | 43 +++++++++++++++++++++++--------------- 1 file changed, 26 insertions(+), 17 deletions(-) diff --git a/nf_core/components/info.py b/nf_core/components/info.py index e4a58d1618..f3e5bf617c 100644 --- a/nf_core/components/info.py +++ b/nf_core/components/info.py @@ -229,6 +229,25 @@ def get_remote_yaml(self) -> Optional[dict]: self.remote_location = self.modules_repo.remote_url return yaml.safe_load(file_contents) + def generate_params_table(self, type) -> Table: + "Generate a rich table for inputs and outputs" + table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) + table.add_column(f":inbox_tray: {type}") + table.add_column("Description") + if self.component_type == "modules": + table.add_column("Pattern", justify="right", style="green") + elif self.component_type == "subworkflows": + table.add_column("Structure", justify="right", style="green") + return table + + def get_channel_structure(self, structure: dict) -> str: + "Get the structure of a channel" + structure_str = "" + for key, info in structure.items(): + pattern = f" - {info['pattern']}" if info.get("pattern") else "" + structure_str += f"{key} ({info['type']}{pattern})" + return structure_str + def generate_component_info_help(self): """Take the parsed meta.yml and generate rich help. @@ -277,14 +296,9 @@ def generate_component_info_help(self): # Inputs if self.meta.get("input"): - inputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) - inputs_table.add_column(":inbox_tray: Inputs") - inputs_table.add_column("Description") - if self.component_type == "modules": - inputs_table.add_column("Pattern", justify="right", style="green") - elif self.component_type == "subworkflows": - inputs_table.add_column("Structure", justify="right", style="green") - for input in self.meta["input"]: + inputs_table = self.generate_params_table("Inputs") + for i, input in enumerate(self.meta["input"]): + inputs_table.add_row(f"[italic]input[{i}][/]", "", "") if self.component_type == "modules": for element in input: for key, info in element.items(): @@ -298,23 +312,18 @@ def generate_component_info_help(self): inputs_table.add_row( f"[orange1 on black] {key} [/][dim i]", Markdown(info["description"] if info["description"] else ""), - info.get("structure", ""), + self.get_channel_structure(info["structure"]) if info.get("structure") else "", ) renderables.append(inputs_table) # Outputs if self.meta.get("output"): - outputs_table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0) - outputs_table.add_column(":outbox_tray: Outputs") - outputs_table.add_column("Description") - if self.component_type == "modules": - inputs_table.add_column("Pattern", justify="right", style="green") - elif self.component_type == "subworkflows": - inputs_table.add_column("Structure", justify="right", style="green") + outputs_table = self.generate_params_table("Outputs") for output in self.meta["output"]: if self.component_type == "modules": for ch_name, elements in output.items(): + outputs_table.add_row(f"{ch_name}", "", "") for element in elements: for key, info in element.items(): outputs_table.add_row( @@ -327,7 +336,7 @@ def generate_component_info_help(self): outputs_table.add_row( f"[orange1 on black] {key} [/][dim i]", Markdown(info["description"] if info["description"] else ""), - info.get("structure", ""), + self.get_channel_structure(info["structure"]) if info.get("structure") else "", ) renderables.append(outputs_table)