MultiQC: summarize analysis results for multiple tools and samples in a single report

MultiQC v1.23

Bug fixes, integration of pytest and mypy, and one new module.

From the user perspective, this is mostly a maintenance release, containing several important bugfixes, plus minor improvements and a new module - Glimpse.

For developers, there are two significant additions to the CI workflow:

• pytest, along with unit tests covering the core library,
• and mypy, along with ensuring that the core codebase is fully type-annotated.

The core unit tests are located in the multiqc/tests folder, and the module tests are located in the corresponding multiqc/modules/*/tests subfolders. The CI workflows are refactored to separate the integration tests and the unit tests, to improve the granularity and parallelization. The tests are discovered and executed with pytest, and the coverage is reported by codecov.

The multiqc/tests subfolder has several test files that cover most of the core library. It also has a test_modules_run.py tests that checks that every module didn't crash when being run on the corresponding data in test-data, and added something into the report. That is somewhat of a blanket test for modules, that doesn't check if the modules logic worked correctly. For that reason, the users are encouraged to write more comprehensive tests that take the specific module logic into account, and place them in multiqc/modules/*/tests. For some initial examples, consider checking:

• The samtools flagstat test that verifies some logic in the flagstat submodule of the samtools module;
• The picard tools test that checks that every submodule for each Picard tool worked correctly.

Other changes & fixes

Fixes

• Custom content"
  • Multiple fixes of the custom content parsing logic (#2674)
  • Fix parsing custom content submodules with a custom config (#2654)
  • Line plot: fix spreading extra_series between multiple datasets (#2684)
  • Line plot series: allow pass lists instead of x/y tuples to work properly with YAML (#2683)
• Re-enabling the software_version module section (#2670)
• When --no-ansi is set, disable colors in rich_click too (#2678)
• Support CWD path filters ( ./path/...) in config (#2676)
• Fix writing report to stdout with --filename stdout, log to stderr (#2672)
• Interactive use:
  • Reset all config values in config.reset(), even those that are not in config_default.yaml (#2660)
  • Reset config between multiqc.run() calls (#2655)
  • Better handling of calling write_report twice (#2688)

Updates

• Run mypy on core library (#2665)
• Add tests for plot export (#2682)
• Add tests for command line use, including for passing TMPDIR (#2677)
• Custom content: allow hash-fenced table columns (#2649)
• Software versions: parse for sorting, but preserve the original strings (#2671)
• Allow both table-level and column-level custom plot config for table (#2662)

New modules

• Glimpse (#2492)

Module fixes

• Fix parsing kraken vs. bracken: respect num_lines in search patterns (#2657)
• Fix the bbmap/qchist search pattern (#2661)

Module updates

• Picard HsMetrics: support any custom X coverage metrics (#2663)
• Samtools coverage: avoid hard crash for invalid file contents (#2664)

Refactoring

• Abstract code related to temporary directory creation into a separate module (#2675)

Infrastructure

• Use pull-request labels and milestones for changelog generation (#2691)