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Nikos Pappas
phap
Commits
9afff2a1
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9afff2a1
authored
4 years ago
by
Nikos Pappas
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more info on README
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9afff2a1
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@@ -70,7 +70,7 @@ $ conda activate phap
5.30.1
```
##
# Models and d
ata dependencies
per tool
##
D
ata dependencies
*
RaFaH, vHULK, HTP
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@@ -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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