Description

A script to determine whether contamination levels exceed given thresholds for an assembly.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

fai (file)

Assembly summary file

*.(fasta|fa|fna)$

meta2 (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

check_csv (file)

Autofilter summary CSV

*.csv$

Output

Name
Description
Pattern

alarm_file

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

alarm_indicator_file.txt (file)

Alarm indicator file containing information about whether the assembly has passed or failed the contamination check.

alarm_indicator_file.txt

raw_report

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

*raw_report.txt (file)

Raw report containing the results of the contamination check.

*raw_report.txt

indicator_file

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

autofiltering_done_indicator_file.txt (file)

A file indicating that autofiltering has been done - Needed for current system implementation.

autofiltering_done_indicator_file.txt

versions_python

${task.process} (string)

Name of the process

python (string)

Name of the tool

python --version | sed "s/Python //" (eval)

The expression to obtain the version of the tool

versions_autofilter

${task.process} (string)

Name of the process

abnormal_contamination_check (string)

Name of the tool

abnormal_contamination_check.py --version | cut -d" " -f2 (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

Name of the process

python (string)

Name of the tool

python --version | sed "s/Python //" (eval)

The expression to obtain the version of the tool

${task.process} (string)

Name of the process

abnormal_contamination_check (string)

Name of the tool

abnormal_contamination_check.py --version | cut -d" " -f2 (eval)

The expression to obtain the version of the tool

Tools

abnormal_contamination_check Documentation

Determine whether contamination levels exceed given thresholds for an assembly.

License: MIT
Authors