RBT CSV-REPORT

https://img.shields.io/github/issues-pr/snakemake/snakemake-wrappers/bio/rbt/csvreport?label=version%20update%20pull%20requests

Creates an html report of qc data stored in a csv file. For more details, visit https://github.com/rust-bio/rust-bio-tools

Example

This wrapper can be used in the following way:

rule csv_report:
    input:
        # a csv formatted file containing the data for the report
        "report.csv",
    output:
        # path to the resulting report directory
        directory("qc_data"),
    params:
        extra="--sort-column 'contig length'",
    log:
        "logs/rbt-csv-report",
    wrapper:
        "v3.8.0-1-g149ef14/bio/rbt/csvreport"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Software dependencies

  • rust-bio-tools=0.42.0

Input/Output

Input:

  • A csv file containing the qc report

Output:

  • QC report folder including html document and .xlsx file

Authors

  • Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2021, Jan Forster"
__email__ = "jan.forster@uk-essen.de"
__license__ = "MIT"

from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell("rbt csv-report {snakemake.input} {snakemake.output} {extra} {log}")