Implement changes from quarto-notebooks branch

[dltamayo]

Implementing quarto notebooks from @KevinMLanderos since quarto-notebooks branch drifted from main

• Updated env.yml, nextflow.config, README.md
• Added new notebooks
• Old notebooks will be retained for compatibility until new notebooks are fully implemented

Add Quarto Report Notebooks to Pipeline

This PR integrates Quarto report notebooks into the TCRtoolkit pipeline. Below are the implementation instructions.

---

1. New Files — notebooks/

Add the following .qmd files from /lab/home/kmlanderos/projects2/TCRtoolkit/notebooks/:

notebooks/template_qc.qmd
notebooks/template_discovery_brief.qmd
notebooks/template_details_part1.qmd
notebooks/template_details_part2.qmd
notebooks/template_gliph.qmd
notebooks/template_overlap.qmd
notebooks/template_pheno_bulk.qmd
notebooks/template_pheno_sc.qmd
notebooks/template_sample.qmd
notebooks/template_sharing.qmd
notebooks/template_giana.qmd

---

2. env.yml — Add Dependencies

- dash>=2.15.0
- upsetplot=0.9.0

---

3. Rendering — 4 Main Notebooks

After the pipeline finishes, render the 4 main notebooks using the following command (repeated for each):

quarto render <notebook.qmd> \
    -P project_name:$params.project_name \
    -P project_dir:$params.project_dir \
    -P workflow_cmd:'$workflow.commandLine' \
    -P sample_table:$sample_table \
    -P timepoint_col:${params.timepoint_col} \
    -P timepoint_order_col:${params.timepoint_order_col} \
    -P alias_col:${params.alias_col} \
    -P subject_col:${params.subject_col} \
    --to html

timepoint_col, timepoint_order_col, alias_col, and subject_col already have defaults defined in nextflow.config — no changes needed there.

The remaining notebooks (template_pheno_sc, template_pheno_bulk, template_gliph, etc.) are not rendered directly — they are embedded via Quarto's {{< include >}} directive.

---

4. Conditional Sub-Notebook Assembly

Before rendering, copy the relevant main notebook to a working directory and append include lines as needed. Do not modify the source templates directly.

template_discovery_brief.qmd

--input_format value	Append to end of notebook copy
cellranger	{{< include ./template_pheno_sc.qmd >}}
adaptive or airr	{{< include ./template_pheno_bulk.qmd >}}

template_details_part2.qmd

Condition	Append to end of notebook copy
--workflow_level includes patient (e.g. sample,patient,compare)	{{< include ./template_giana.qmd >}}
Patient workflow enabled and --use_gliph2 is set	Also append {{< include ./template_gliph.qmd >}}

Make sure the sub-notebook .qmd files are also present in the same working directory so relative {{< include >}} paths resolve correctly during rendering.

5. README.md

File updated to include patient workflow, pipeline parameters and HTML reports

Co-Authored-By: KevinMLanderos kevinmezalanderos@gmail.com

[github-actions]

Unit Test Results

10 tests  ±0   10 ✅ ±0   2m 51s ⏱️ -16s
 2 suites ±0    0 💤 ±0 
 1 files   ±0    0 ❌ ±0 

Results for commit fa758e2. ± Comparison against base commit e931159.