chore: new release

[visze]

No description provided.

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[Copilot]

Pull request overview

This PR broadens MPRAsnakeflow’s configuration and experiment-counting capabilities (notably adding an NGmerge-based merge path), extends mapping-time filtering options, and substantially expands/refreshes documentation and example resources in preparation for a new release.

Changes:

• Add an experiment-level merge_tool switch with an NGmerge-based merging/counting path (including a shared NGmerge rule template).
• Extend assignment/mapping configuration options (e.g., optional bwa min/max windows, cigar_filter_regex) and adjust design-check window handling.
• Add multiple new dataset example pages and update documentation/config examples accordingly.

Reviewed changes

Copilot reviewed 43 out of 66 changed files in this pull request and generated 14 comments.

Show a summary per file

File	Description
workflow/scripts/attachBCToFastQ.py	Allow multiple --reads/--barcodes pairs (used for NGmerge UMI header attachment).
workflow/scripts/assignment/check_design_file.py	Make --start/--length conditionally required; improve help text and erroring.
workflow/schemas/config.schema.yaml	Update schema for new/changed config keys (design_check window, cigar regex, experiment merge_tool/NGmerge).
workflow/rules/experiment/statistic/counts.smk	Minor fix/formatting; use wc.project in helper inputs.
workflow/rules/experiment/counts/counts_umi.smk	Add NGmerge UMI path (attach UMI to headers + NGmerge + header parsing for counts).
workflow/rules/experiment/counts/counts_noUMI.smk	Add NGmerge no-UMI path for paired reads.
workflow/rules/experiment/counts/counts_merge_ngmerge.smk	New shared NGmerge merge rule template for experiment workflows.
workflow/rules/experiment/counts.smk	Include the new NGmerge template rule file.
workflow/rules/common.smk	Add config pre/post processing and helper typing/validation tweaks.
workflow/rules/assignment/mapping_bwa.smk	Add optional window filtering + optional CIGAR-regex filtering to barcode extraction.
workflow/rules/assignment/mapping_bbmap.smk	Add optional CIGAR-regex filtering to barcode extraction.
workflow/rules/assignment/hybridFWDRead.smk	Formatting-only changes in awk block.
workflow/rules/assignment/common.smk	Add helpers for design_check access and CLI arg formatting.
workflow/rules/assignment.smk	Switch design-check arg construction to new helper functions.
resources/count_basic/experiment_noUMI.csv	New experiment CSV example (no UMI).
resources/count_basic/experiment_FWDUMI.csv	New experiment CSV example (FWD + UMI).
resources/count_basic/experiment_FWD.csv	New experiment CSV example (FWD-only).
docs/index.rst	Add examples overview + new example pages to the docs toctree.
docs/4_examples/plasmid_example.rst	Update heading/formatting and clarify dataset reference.
docs/4_examples/overview.rst	New “Examples Overview” landing page with dataset summaries/links.
docs/4_examples/GSE325670_example.rst	New detailed example page for Hauser et al. dataset.
docs/4_examples/GSE316891_example.rst	New detailed example page for Yan et al. dataset.
docs/4_examples/GSE307247_example.rst	New detailed example page for Koplik et al. dataset.
docs/4_examples/GSE306816_example.rst	New detailed example page for Zhang et al. dataset.
docs/4_examples/GSE293036_example.rst	New detailed example page for Granitto et al. dataset.
docs/4_examples/GSE284330_example.rst	New detailed example page for Zaratiana et al. dataset.
docs/4_examples/GSE271608_example.rst	New detailed example page for Zahm et al. dataset.
docs/4_examples/count_example1.rst	Update Klein et al. link to DOI.
docs/4_examples/complex_readstructure_example.rst	Update title/anchors and adjust resource guidance (memory).
docs/4_examples/combined_example1.rst	Update Klein et al. link to DOI.
docs/4_examples/assignment_example1.rst	Update Klein et al. link to DOI.
docs/3_further_documentation/adapter.rst	Grammar/clarity improvements.
docs/2_workflows/experiment.rst	Correct multiple typos/grammar in workflow documentation.
docs/1_getting_started/config.rst	Document new/changed config keys (merge_tool, cigar_filter_regex, design_check window).
config/example_count.yaml	Bump example config version.
config/example_config.yaml	Bump example config version.
config/example_assignment_pbmm2.yaml	Bump example config version; move window to design_check.
config/example_assignment_exact_linker.yaml	Bump example config version.
config/example_assignment_exact_lazy.yaml	Bump example config version.
config/example_assignment_bwa.yaml	Bump example config version.
config/example_assignment_bbmap.yaml	Bump example config version; move window to design_check.
.github/release-please-config.json	Configure changelog sections for release-please.
.github/copilot-instructions.md	Update “Adding a New Rule” snippet to match current style/structure.

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[Copilot]

Pull request overview

Copilot reviewed 46 out of 69 changed files in this pull request and generated 14 comments.

Comments suppressed due to low confidence (1)

docs/4_examples/GSE284330_example.rst:165

• This paragraph contains multiple typos/grammar issues (e.g. meadian, less then, a exact, satting, highlits) that reduce readability of the rendered docs.

* :code:`results/experiments/GSE284330/reporter_experiment.barcode.HepG2Sub1.GSE284330.BCthreshold1.all.tsv.gz`

You should also inspect the QC report in the same directory, or have a look `here <https://htmlpreview.github.io/?https://github.com/kircherlab/MPRAsnakeflow/blob/master/docs/4_examples/GSE284330.experiment.qc_report.HepG2Sub1.BCthreshold1.html>`_. As expected we have a meadian BC of 1. We also see that we only get a library coverage of less then 20%. This is expected because this assay is not really designed for barcode-based counting. We are doing a exact mapping of 200bp sequenced oligos. The assay is more similar to a STARR-seq like assay where the oligos themselves are sequenced and counted. Therefore, we have a lot of oligos that are not covered by any read and many reads that do not match any oligo. This example is therefore not ideal for MPRAsnakeflow, but it demonstrates how to use the workflow can be used in that satting and highlits potential optimizations for future versions of the workflow, like implementing a mapping strategy for the experiment sub-workflow.

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter

[github-actions]

Super-linter summary

Language	Validation result
JSON	Pass ✅
PYTHON_FLAKE8	Pass ✅
SNAKEMAKE_SNAKEFMT	Pass ✅
YAML	Pass ✅

All files and directories linted successfully

For more information, see the GitHub Actions workflow run

Powered by Super-linter