pyppl-report 0.5.0rc1

A report generating system for PyPPL

pyppl_report

A report generating system for PyPPL

Installation

Requires pandoc 2.7+ (and wkhtmltopdf 0.12.4+ when creating PDF reports)

pyppl_report requires pandoc/wkhtmltopdf to be installed in $PATH

pip install pyppl_report

Usage

Specifiation of template

pPyClone.config.report_template = """
## {{title}}

PyClone[1] is a tool using Probabilistic model for inferring clonal population structure from deep NGS sequencing.

![Similarity matrix]({{path.join(job.o.outdir, "plots/loci/similarity_matrix.svg")}})

```table
caption: Clusters
file: "{{path.join(job.o.outdir, "tables/cluster.tsv")}}"
rows: 10
```

[1]: Roth, Andrew, et al. "PyClone: statistical inference of clonal population structure in cancer." Nature methods 11.4 (2014): 396.
"""

# or use a template file

pPyClone.config.report_template = "file:/path/to/template.md"

Generating report

PyPPL().start(pPyClone).run().report('/path/to/report', title = 'Clonality analysis using PyClone')

# or save report in a directory
PyPPL(name = 'Awesome-pipeline').start(pPyClone).run().report('/path/to/')
# report generated at ./Awesome-pipeline.report.html

Extra data for rendering

You can generate a toml file named job.report.data.toml under <job.outdir> with extra data to render the report template. Beyond that, proc attributes and args can also be used.

For example: job.report.data.toml:

description = 'A awesome report for job 1'

Then in your template, you can use it:

## {{jobs[0].description}}

Showing tables with csv/tsv file

```table
caption    : An awesome table
file       : /path/to/csv/tsv/file
header     : true
width      : 1   # width of each column
total_width: .8  # total width of the table
align      : default # alignment of each column
rows       : 10  # max rows to show
cols       : 0   # max cols to show, default: 0 (show all)
csvargs    : # csvargs for `csv.read`
	dialect: unix
	delimiter: "\t"

You may also specify width and align for individual columns:

width = [.1, .2, .1]

References

We use [1], [2] ... to link to the references, so HTML links have to be in-place (in the format of [text](link) instead of [text][link-index]). All references from different processes will be re-ordered and combined.

Advanced usage

ReadTheDocs