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Commit 27916d53 authored by Nikos Pappas's avatar Nikos Pappas
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update README for report

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......@@ -312,3 +312,18 @@ doing its magic.
Logs capturing stdout and stderr during execution of each rule can be found in
`workdir/logs/<sample_id>/*.log` files.
### Report
After successful execution of the workflow, a (basic) html report with summary
statistics can be produced with
```
(phap)$ snakemake --use-singularity \
--singularity-args "-B path/to/data_dir:/data" --report phap.html
```
This will produce a `phap.html` file and a `report` directory at the root dir.
The `report` directory contains the two main aggregated tables from
[the per sample results directory](#per-sample) rendered as html documents.
These are accessible under the Results category of the main `phap.html`.
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