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diff --git a/data/modules/bases2fastq/README.md b/data/modules/bases2fastq/README.md index fa21bea4..0abe70f5 100644 --- a/data/modules/bases2fastq/README.md +++ b/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//_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//_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. diff --git a/data/modules/bases2fastq/SingleEndNoProject/RunStats.json b/data/modules/bases2fastq/SingleEndNoProject/RunStats.json new file mode 100644 index 00000000..0ec06eea --- /dev/null +++ b/data/modules/bases2fastq/SingleEndNoProject/RunStats.json @@ -0,0 +1 @@ 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