RBT CSV-REPORT
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:
"v5.3.0-16-g710597c/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=0.42.2
Input/Output
Input:
A csv file containing the qc report
Output:
QC report folder including html document and .xlsx file
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}")