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Commit 9afff2a1 authored by Nikos Pappas's avatar Nikos Pappas
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more info on README

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......@@ -70,7 +70,7 @@ $ conda activate phap
5.30.1
```
### Models and data dependencies per tool
## Data dependencies
* RaFaH, vHULK, HTP
......@@ -335,22 +335,24 @@ doing its magic.
</details>
### Logs
## Logs
Logs capturing stdout and stderr during execution of each rule can be found in
`workdir/logs/<sample_id>/*.log` files.
### Report
## Report
After successful execution of the workflow, a (basic) html report with summary
statistics can be produced with
**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.
This will produce a `phap.html` file, making use of the information in the
`report` directory.
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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