Added new run- and project-level json templates for Bases2Fastq

data/modules/bases2fastq/README.md

@@ -1,14 +1,36 @@
-Real dataset generated from AVITI sequencing by Bases2fastq v1.4.0 (only files neccessay for MultiQC included)
+Real dataset generated from AVITI sequencing by Bases2fastq v1.4.0 (only files necessary for MultiQC included), plus template run layouts for run-level and project-level outputs.
 
-This directory contains multiple bases2fastq output directories.
+This directory contains multiple bases2fastq output directories (run roots). Each subdirectory is a separate run root: it may contain run-level `RunStats.json`, optional `RunManifest.json`, and optionally `Samples/<ProjectName>/<ProjectName>_RunStats.json` for project-level data.
 
-Running multiqc on any of the sub-directories single MultiQC report, spanning multiple runs and multiple samples.
+## How to run MultiQC
+
+**Option 1 – run on the whole module directory** (all run roots at once):
+
+```bash
+multiqc test-data/data/modules/bases2fastq/ --filename bases2fastq --force
+```
+
+**Option 2 – run on a single run root** (typical for project-level: change into that directory or pass it):
 
 ```bash
-multiqc Cloudbreak-DVT-ecoli-wgs-2x150/ --filename Cloudbreak-DVT-ecoli-wgs-2x150 --force
-multiqc Cloudbreak-DVT-human-wgs-2x150/ --filename Cloudbreak-DVT-human-wgs-2x150 --force
-multiqc Cloudbreak-DVT-human-rnaseq-2x75/ --filename Cloudbreak-DVT-human-rnaseq-2x75 --force
+# Run-level only (no project, no RunManifest)
+multiqc test-data/data/modules/bases2fastq/PairedEndNoProject/ --filename PairedEndNoProject --force
+
+# Run + DefaultProject (RunManifest at run root; project file in Samples/DefaultProject/)
+multiqc test-data/data/modules/bases2fastq/PairedEndDefaultProject/ --filename PairedEndDefaultProject --force
+
+# Multiple projects in one run
+multiqc test-data/data/modules/bases2fastq/PairedEndProjects/ --filename PairedEndProjects --force
 ```
-* `Cloudbreak-DVT-ecoli-wgs-2x150/` - contains a 96plex of Ecoli WGS lirbaries, sequenced on a single AVITI run, 1 run total.
-* `Cloudbreak-DVT-human-wgs-2x150/` - contains a 2plex of Human WGS lirbaries, sequenced on a single AVITI run, 2 runs total.
-* `Cloudbreak-DVT-human-rnaseq-2x75/` - contains a 16plex of Human RNASEQ lirbaries, sequenced on a single AVITI run, 10 runs total.
+
+## Contents
+
+* **WGS/** – Real AVITI/Bases2fastq run (run-level only).
+* **WES/** – Real AVITI/Bases2fastq run (run-level only).
+* **PairedEndNoProject/** – Template: run-level `RunStats.json` only.
+* **SingleEndNoProject/** – Template: run-level `RunStats.json` only (single-end).
+* **PairedEndDefaultProject/** – Template: run-level + `RunManifest.json` + `Samples/DefaultProject/DefaultProject_RunStats.json`.
+* **PairedEndDefaultProjectAdapter/**, **PairedEndDefaultProjectTwoAdapter/**, **PairedEndDefaultProjectUltraQ/** – Variants with DefaultProject and RunManifest.
+* **PairedEndProjects/** – Template: run-level + RunManifest + multiple projects (`Samples/Project1/`, `Project2/`, …).
+
+Run-level data lives in `RunStats.json` at the run root. When project-level outputs exist, they live under `Samples/<ProjectName>/<ProjectName>_RunStats.json`, and `RunManifest.json` is at the run root (or next to the project file). Use option 2 when you want a report for one run root; use option 1 to aggregate all run roots in one report.