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c19671dca9
* feat(subworkflows): Add align_bowtie2 subworkflow For testing CI setup * test(align_bowtie2): Add initial list of changes to test * test(align_bowtie2): Add initial test * refactor: Use tags to run subworkflows ci For every underlying module used by workflow and allow the modules pytest-modules definition be the source of truth. * refactor: Use individual directories for subworkflows * docs(align_bowtie2): Add initial meta.yml Copied most of it from the bowtie2/align module. * fix(align_bowtie2): Fix module include paths * test(bam_sort_samtools): Add initial test * ci(bam_sort_samtools): Add modules that trigger the tag * test(bam_stats_samtools): Add initial test * ci(bam_stats_samtools): Add keys to pick up changes * docs(bam_samtools): Add initial meta.yml * test(align_bowtie2): Fix path to subworkflow * test(align_bowtie2): Update entry point * fix(bam_sort_samtools): Update include paths * test(bam_sort_samtools): Fix path * style: Clean up addParams * test(samtools_sort): Add suffix for test * test(align_bowtie2): Add samtools_options for suffix * test(bam_stats_samtools): Update path * test(bam_stats_samtools): Use stats input Otherwise it's just an example of how it's used in the bam_sort_samtools subworkflow * ci(linting): Skip module linting of subworkflows * ci(linting): Clean up startsWith statement * test(bam_stats_samtools): Use single end test data for single end test * test(bam_stats_samtools): Add expected files * test(align_bowtie2): Add paired-end test * test(align_bowtie2): Sort order of output * test(align_bowtie2): Update hashes * docs(align_bowtie2): Fix typo * test(align_bowtie2): Update samtools output names * test(align_bowtie2): Remove md5sums for bam/bai * feat(subworkflows): Add nextflow.configs These can be used for default settings in the future. They can then be included in the conf/modules.config so that the params don't have to be duplicated in the root nextflow.config. * docs(subworkflows): Include modules instead of tools * fix: Update to versions * chore(align_bowtie2): Remove duplicate tag * style: Format yamls * test(subworkflows): Only check versions for modules * chore: Update subworkflows to match rnaseq dev * fix(subworkflows): Update paths * fix(bam_sort_samtools): Fix sort parameters for testing * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * docs: Update TODOs with a message * ci: Try using a matrix for strategy * ci: Try passing an array * Revert "ci: Try passing an array" This reverts commit d3611fcd8332bbb9a8501e8dd299d0a623aaecaa. Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
57 lines
2.1 KiB
Python
57 lines
2.1 KiB
Python
from pathlib import Path
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import pytest
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import yaml
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import re
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from textwrap import dedent
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def _get_workflow_names():
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"""Get all names of all workflows which have a test.yml in the tests directory.
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To do so, recursively finds all test.yml files and parses their content.
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"""
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here = Path(__file__).parent.resolve()
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pytest_workflow_files = here.glob("modules/**/test.yml")
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for f in pytest_workflow_files:
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# test_config = yaml.safe_load(f.read_text())
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test_config = yaml.load(f.read_text(), Loader=yaml.BaseLoader)
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for workflow in test_config:
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yield workflow["name"]
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@pytest.mark.workflow(*_get_workflow_names())
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def test_ensure_valid_version_yml(workflow_dir):
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workflow_dir = Path(workflow_dir)
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software_name = workflow_dir.name.split("_")[0].lower()
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try:
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versions_yml_file = workflow_dir / f"output/{software_name}/versions.yml"
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versions_yml = versions_yml_file.read_text()
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except FileNotFoundError:
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raise AssertionError(
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dedent(
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f"""\
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`versions.yml` not found in the output directory.
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Expected path: `{versions_yml_file}`
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This can have multiple reasons:
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* The test-workflow failed before a `versions.yml` could be generated.
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* The workflow name in `test.yml` does not start with the tool name.
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"""
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)
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)
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assert (
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"END_VERSIONS" not in versions_yml
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), "END_VERSIONS detected in versions.yml. This is a sign of an ill-formatted HEREDOC"
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# Raises an exception if yaml is not valid
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versions = yaml.safe_load(versions_yml)
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assert (
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len(versions) == 1
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), "The top-level of versions.yml must contain exactly one entry: the process name as dict key"
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software_versions = next(iter(versions.values()))
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assert len(software_versions), "There must be at least one version emitted."
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for tool, version in software_versions.items():
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assert re.match(
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r"^\d+.*", str(version)
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), f"Version number for {tool} must start with a number. "
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