Workflow scripts

Each ordered workflow-stage page includes Previous, Workflow contents, and Next links at both the top and bottom.

These scripts are organized by analytical stage. They are public-release adaptations of preserved project scripts, not newly executed analyses.

• week1_training/: method record for the separate chromosome-22 exercise.
• week2_consensus_counts/: consensus construction, paired-fragment counting, and clean-matrix creation.
• week2_differential_accessibility/: primary donor-aware DESeq2 analysis and nominal sensitivity summaries.
• week3_exploratory/: nominal-candidate annotation, g:Profiler input preparation, and HOMER sensitivity analysis.

The scripts intentionally refuse to overwrite existing output locations. Review all paths and software requirements before execution.

Relationship to the reusable tutorial

The step-by-step tutorial explains the decisions, inputs, outputs, and validation gates around each stage. The scripts in this directory remain the worked internship implementation and contain deliberate case-study checks, including the recorded sample order and design. They are not advertised as a universal push-button pipeline.

Tutorial stage	Case-study implementation
Raw-read QC through peak calling	week1_training/README.md and docs/METHODS.md
Consensus regions and fragment counting	week2_consensus_counts/
Differential accessibility	week2_differential_accessibility/
Annotation and enrichment	week3_exploratory/

For a new dataset, begin with the blank files under the config/templates/ guide and revise the scripts only after the new metadata, reference resources, thresholds, and statistical design have been justified.