From 34ead3efa80d57652237878f64b7870c1a4d382e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 13 Sep 2024 16:46:16 +0200 Subject: [PATCH 01/13] remove try-catch blocks from nextflow.config --- CHANGELOG.md | 1 + nf_core/pipeline-template/nextflow.config | 13 +++---------- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 68399a9c0b..a1cab78972 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -40,6 +40,7 @@ - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099)) - Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037)) - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176)) +- Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167)) ### Linting diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 3e301f0b0b..28b7d7963e 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -186,18 +186,11 @@ profiles { {% if nf_core_configs -%} // Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load {{ name }} custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config") -} +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" {% endif -%} // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile From 930933b9ee077160907b61a2d5a7fcd3b776ba0f Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 11:52:34 +0200 Subject: [PATCH 02/13] change the name of tmp pipeline to be consistent with all tests --- tests/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/utils.py b/tests/utils.py index 1d5a8a115d..e04a4b038e 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -104,7 +104,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: tmp_dir = Path(tempfile.TemporaryDirectory().name) root_repo_dir = Path(__file__).resolve().parent.parent template_dir = root_repo_dir / "nf_core" / "pipeline-template" - pipeline_name = "mypipeline" + pipeline_name = "testpipeline" pipeline_dir = tmp_dir / pipeline_name pipeline_dir.mkdir(parents=True) @@ -114,7 +114,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: org_path="nf-core", lint=None, template=NFCoreTemplateConfig( - name="mypipeline", + name="testpipeline", author="me", description="it is mine", org="nf-core", From e6fdba8886cfdf5bbcb7cef2c6b319da7825a3a9 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 12:19:46 +0200 Subject: [PATCH 03/13] update nextflow_config linting to include the new includeconfig line --- nf_core/pipelines/lint/nextflow_config.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 14e91cc609..dd45621bc6 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -346,7 +346,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`") # Check that lines for loading custom profiles exist - lines = [ + old_lines = [ r"// Load nf-core custom profiles from different Institutions", r"try {", r'includeConfig "${params.custom_config_base}/nfcore_custom.config"', @@ -354,11 +354,19 @@ def nextflow_config(self) -> Dict[str, List[str]]: r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")', r"}", ] + lines = [ + r"// Load nf-core custom profiles from different Institutions", + r'''includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"''', + ] path = Path(self.wf_path, "nextflow.config") i = 0 with open(path) as f: for line in f: - if lines[i] in line: + if old_lines[i] in line: + i += 1 + if i == len(old_lines): + break + elif lines[i] in line: i += 1 if i == len(lines): break @@ -366,6 +374,12 @@ def nextflow_config(self) -> Dict[str, List[str]]: i = 0 if i == len(lines): passed.append("Lines for loading custom profiles found") + elif i == len(old_lines): + failed.append( + "Old lines for loading custom profiles found. File should contain: ```groovy\n{}".format( + "\n".join(lines) + ) + ) else: lines[2] = f"\t{lines[2]}" lines[4] = f"\t{lines[4]}" From 27093939c2dec3d770a97ea17222ffbe7c2b6934 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 13 Sep 2024 16:46:16 +0200 Subject: [PATCH 04/13] remove try-catch blocks from nextflow.config --- CHANGELOG.md | 1 + nf_core/pipeline-template/nextflow.config | 13 +++---------- 2 files changed, 4 insertions(+), 10 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6a11aee515..b1c5463a9f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -41,6 +41,7 @@ - Remove if/else block to include `igenomes.config` ([#3168](https://github.com/nf-core/tools/pull/3168)) - Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037)) - Fixed release announcement hashtags for Mastodon ([#3099](https://github.com/nf-core/tools/pull/3176)) +- Remove try/catch blocks from `nextflow.config` ([#3167](https://github.com/nf-core/tools/pull/3167)) ### Linting diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 39c3521363..dc2aea0b72 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -186,18 +186,11 @@ profiles { {% if nf_core_configs -%} // Load nf-core custom profiles from different Institutions -try { - includeConfig "${params.custom_config_base}/nfcore_custom.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") -} +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load {{ name }} custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/{{ short_name }}.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config") -} +// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" {% endif -%} // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile From b1df038c263bd8893d7971e0cfe30dac746f86d1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 11:52:34 +0200 Subject: [PATCH 05/13] change the name of tmp pipeline to be consistent with all tests --- tests/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/utils.py b/tests/utils.py index 6f4b73cccc..022b91227f 100644 --- a/tests/utils.py +++ b/tests/utils.py @@ -113,7 +113,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: tmp_dir = Path(tempfile.TemporaryDirectory().name) root_repo_dir = Path(__file__).resolve().parent.parent template_dir = root_repo_dir / "nf_core" / "pipeline-template" - pipeline_name = "mypipeline" + pipeline_name = "testpipeline" pipeline_dir = tmp_dir / pipeline_name pipeline_dir.mkdir(parents=True) @@ -123,7 +123,7 @@ def create_tmp_pipeline(no_git: bool = False) -> Tuple[Path, Path, str, Path]: org_path="nf-core", lint=None, template=NFCoreTemplateConfig( - name="mypipeline", + name="testpipeline", author="me", description="it is mine", org="nf-core", From 7e738eab0ed726ea21d007822a30e396a62c8ded Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 16 Sep 2024 12:19:46 +0200 Subject: [PATCH 06/13] update nextflow_config linting to include the new includeconfig line --- nf_core/pipelines/lint/nextflow_config.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/lint/nextflow_config.py b/nf_core/pipelines/lint/nextflow_config.py index 14e91cc609..dd45621bc6 100644 --- a/nf_core/pipelines/lint/nextflow_config.py +++ b/nf_core/pipelines/lint/nextflow_config.py @@ -346,7 +346,7 @@ def nextflow_config(self) -> Dict[str, List[str]]: failed.append(f"Config `params.custom_config_base` is not set to `{custom_config_base}`") # Check that lines for loading custom profiles exist - lines = [ + old_lines = [ r"// Load nf-core custom profiles from different Institutions", r"try {", r'includeConfig "${params.custom_config_base}/nfcore_custom.config"', @@ -354,11 +354,19 @@ def nextflow_config(self) -> Dict[str, List[str]]: r'System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")', r"}", ] + lines = [ + r"// Load nf-core custom profiles from different Institutions", + r'''includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"''', + ] path = Path(self.wf_path, "nextflow.config") i = 0 with open(path) as f: for line in f: - if lines[i] in line: + if old_lines[i] in line: + i += 1 + if i == len(old_lines): + break + elif lines[i] in line: i += 1 if i == len(lines): break @@ -366,6 +374,12 @@ def nextflow_config(self) -> Dict[str, List[str]]: i = 0 if i == len(lines): passed.append("Lines for loading custom profiles found") + elif i == len(old_lines): + failed.append( + "Old lines for loading custom profiles found. File should contain: ```groovy\n{}".format( + "\n".join(lines) + ) + ) else: lines[2] = f"\t{lines[2]}" lines[4] = f"\t{lines[4]}" From e46779b6b8709af658c43ed5533603db306231e1 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:04:28 +0200 Subject: [PATCH 07/13] add test on pipeline release to check that custom configs are included --- nf_core/pipeline-template/nextflow.config | 2 +- nf_core/pipelines/lint/__init__.py | 4 ++- nf_core/pipelines/lint/included_configs.py | 37 ++++++++++++++++++++++ 3 files changed, 41 insertions(+), 2 deletions(-) create mode 100644 nf_core/pipelines/lint/included_configs.py diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index dc2aea0b72..4c816a2a2c 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -190,7 +190,7 @@ includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${pa // Load {{ name }} custom profiles from different institutions. // TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" +// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/{{ short_name }}.config" : "/dev/null" {% endif -%} // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index 6d27351b62..8cc7c37cb2 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -37,6 +37,7 @@ from .configs import base_config, modules_config from .files_exist import files_exist from .files_unchanged import files_unchanged +from .included_configs import included_configs from .merge_markers import merge_markers from .modules_json import modules_json from .modules_structure import modules_structure @@ -101,6 +102,7 @@ class PipelineLint(nf_core.utils.Pipeline): system_exit = system_exit template_strings = template_strings version_consistency = version_consistency + included_configs = included_configs def __init__( self, wf_path, release_mode=False, fix=(), key=None, fail_ignored=False, fail_warned=False, hide_progress=False @@ -152,7 +154,7 @@ def _get_all_lint_tests(release_mode): "base_config", "modules_config", "nfcore_yml", - ] + (["version_consistency"] if release_mode else []) + ] + (["version_consistency", "included_configs"] if release_mode else []) def _load(self) -> bool: """Load information about the pipeline into the PipelineLint object""" diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py new file mode 100644 index 0000000000..9d4eb1f990 --- /dev/null +++ b/nf_core/pipelines/lint/included_configs.py @@ -0,0 +1,37 @@ +from pathlib import Path + + +def included_configs(self): + """Check that the pipeline nextflow.config includes the pipeline custom configs. + + If the include line is uncommented, the test passes. + If the include line is commented, the test fails. + If the include line is missing, the test warns. + + Can be skipped by adding the following to the .nf-core.yml file: + lint: + included_configs: False + """ + passed = [] + failed = [] + warned = [] + + config_file = Path(self.wf_path / "nextflow.config") + + with open(config_file) as fh: + config = fh.read() + print(self.pipeline_name) + if ( + f"// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + in config + ): + failed.append("Pipeline config does not include custom configs. Please uncomment the includeConfig line.") + elif ( + "includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + in config + ): + passed.append("Pipeline config includes custom configs.") + else: + warned.append("Pipeline config does not include custom configs. Please add the includeConfig line.") + + return {"passed": passed, "failed": failed, "warned": warned} From 70b231e9ee4eb1361f5bfb0cc47aec41bc73f849 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:43:28 +0200 Subject: [PATCH 08/13] fix tests by uncommenting includeConfig statements --- .github/actions/create-lint-wf/action.yml | 6 ++++++ .github/workflows/create-lint-wf.yml | 5 +++++ .github/workflows/create-test-lint-wf-template.yml | 5 +++++ nf_core/pipelines/create/template_features.yml | 1 + nf_core/pipelines/lint/included_configs.py | 1 - 5 files changed, 17 insertions(+), 1 deletion(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 8760901db1..7cc6f85d4f 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -53,6 +53,12 @@ runs: run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + shell: bash + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX shell: bash diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 1a3e283d00..190cd01170 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -78,6 +78,11 @@ jobs: run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Run the other nf-core commands - name: nf-core pipelines list run: nf-core --log-file log.txt pipelines list diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 1fb521b4bb..10aeccd297 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -137,6 +137,11 @@ jobs: run: find my-prefix-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \; working-directory: create-test-lint-wf + # Uncomment includeConfig statement + - name: uncomment include config + run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + working-directory: create-lint-wf + # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX run: find my-prefix-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \; diff --git a/nf_core/pipelines/create/template_features.yml b/nf_core/pipelines/create/template_features.yml index 6f476cdfbe..55bb3b0b3e 100644 --- a/nf_core/pipelines/create/template_features.yml +++ b/nf_core/pipelines/create/template_features.yml @@ -120,6 +120,7 @@ nf_core_configs: - "custom_config" - "params.custom_config_version" - "params.custom_config_base" + included_configs: False nfcore_pipelines: False custom_pipelines: True is_nfcore: diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py index 9d4eb1f990..6cfeb3f8a5 100644 --- a/nf_core/pipelines/lint/included_configs.py +++ b/nf_core/pipelines/lint/included_configs.py @@ -20,7 +20,6 @@ def included_configs(self): with open(config_file) as fh: config = fh.read() - print(self.pipeline_name) if ( f"// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" in config From 3a0a8ca33cc876bfb6299ded1b09f1b9cd4e4dcd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 11:56:51 +0200 Subject: [PATCH 09/13] fix sed commands --- .github/actions/create-lint-wf/action.yml | 2 +- .github/workflows/create-lint-wf.yml | 2 +- .github/workflows/create-test-lint-wf-template.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/actions/create-lint-wf/action.yml b/.github/actions/create-lint-wf/action.yml index 7cc6f85d4f..ecd0eef873 100644 --- a/.github/actions/create-lint-wf/action.yml +++ b/.github/actions/create-lint-wf/action.yml @@ -56,7 +56,7 @@ runs: # Uncomment includeConfig statement - name: uncomment include config shell: bash - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Replace zenodo.XXXXXX to pass readme linting diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml index 190cd01170..e0b4c67cfc 100644 --- a/.github/workflows/create-lint-wf.yml +++ b/.github/workflows/create-lint-wf.yml @@ -80,7 +80,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Run the other nf-core commands diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 10aeccd297..86d6b3f6b7 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -139,7 +139,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: sed -i 's/\/\/ includeConfig/includeConfig/' nf-core-testpipeline/nextflow.config + run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-lint-wf # Replace zenodo.XXXXXX to pass readme linting From c779bf4197ae545527cc4251ce27aeb3ee011c3b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:10:19 +0200 Subject: [PATCH 10/13] formatted string --- nf_core/pipelines/lint/included_configs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipelines/lint/included_configs.py b/nf_core/pipelines/lint/included_configs.py index 6cfeb3f8a5..75c4594f41 100644 --- a/nf_core/pipelines/lint/included_configs.py +++ b/nf_core/pipelines/lint/included_configs.py @@ -26,7 +26,7 @@ def included_configs(self): ): failed.append("Pipeline config does not include custom configs. Please uncomment the includeConfig line.") elif ( - "includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" + f"includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? \"${{params.custom_config_base}}/pipeline/{self.pipeline_name}.config\"" in config ): passed.append("Pipeline config includes custom configs.") From d625d923933294b9da93cc63de0b4beccdd35752 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:16:03 +0200 Subject: [PATCH 11/13] test output directory typo --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index 86d6b3f6b7..debbf8e691 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -140,7 +140,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; - working-directory: create-lint-wf + working-directory: create-test-lint-wf # Replace zenodo.XXXXXX to pass readme linting - name: replace zenodo.XXXXXX From 19d21bb91ab2c765406224417db417189ece6af2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:19:38 +0200 Subject: [PATCH 12/13] fix more output directory errors --- .github/workflows/create-test-lint-wf-template.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/create-test-lint-wf-template.yml b/.github/workflows/create-test-lint-wf-template.yml index debbf8e691..d8df2f6905 100644 --- a/.github/workflows/create-test-lint-wf-template.yml +++ b/.github/workflows/create-test-lint-wf-template.yml @@ -139,7 +139,7 @@ jobs: # Uncomment includeConfig statement - name: uncomment include config - run: find nf-core-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; + run: find my-prefix-testpipeline -type f -exec sed -i 's/\/\/ includeConfig/includeConfig/' {} \; working-directory: create-test-lint-wf # Replace zenodo.XXXXXX to pass readme linting From 5f367d18ffa4274ba8eb3084cf94abe6c10e19c2 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Mon, 30 Sep 2024 12:32:51 +0200 Subject: [PATCH 13/13] generate API docs --- docs/api/_src/pipeline_lint_tests/included_configs.md | 5 +++++ docs/api/_src/pipeline_lint_tests/index.md | 2 ++ 2 files changed, 7 insertions(+) create mode 100644 docs/api/_src/pipeline_lint_tests/included_configs.md diff --git a/docs/api/_src/pipeline_lint_tests/included_configs.md b/docs/api/_src/pipeline_lint_tests/included_configs.md new file mode 100644 index 0000000000..f68f7da25e --- /dev/null +++ b/docs/api/_src/pipeline_lint_tests/included_configs.md @@ -0,0 +1,5 @@ +# included_configs + + ```{eval-rst} + .. automethod:: nf_core.pipelines.lint.PipelineLint.included_configs + ``` diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md index 3575c08db4..4dd93442d2 100644 --- a/docs/api/_src/pipeline_lint_tests/index.md +++ b/docs/api/_src/pipeline_lint_tests/index.md @@ -7,6 +7,7 @@ - [base_config](./base_config/) - [files_exist](./files_exist/) - [files_unchanged](./files_unchanged/) + - [included_configs](./included_configs/) - [merge_markers](./merge_markers/) - [modules_config](./modules_config/) - [modules_json](./modules_json/) @@ -16,6 +17,7 @@ - [nfcore_yml](./nfcore_yml/) - [pipeline_name_conventions](./pipeline_name_conventions/) - [pipeline_todos](./pipeline_todos/) + - [plugin_includes](./plugin_includes/) - [readme](./readme/) - [schema_description](./schema_description/) - [schema_lint](./schema_lint/)