Description

A tool to filter FASTA headers and filter sequences by length.

Input

Name
Description
Pattern

meta (map)

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

fai (file)

Input assembly FAI index file

*.fai

Output

Name
Description
Pattern

stats

meta (map)

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

*_stats.json (file)

Stats file detailing changes

*_stats.json

mapping_file

meta (map)

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

*_mapping.txt (file)

Mapping file linking old FASTA headers to new ones

*_mapping.txt

new_scaffolds

meta (map)

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

*_new_scaffolds.txt (file)

Text file containing only the new scaffold names

*_new_scaffolds.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_filter_fasta

${task.process} (string)

Name of the process

filter_fasta (string)

Name of the tool

filter_fasta.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

filter_fasta (string)

Name of the tool

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

The expression to obtain the version of the tool

Tools

filter_fasta Documentation

Filter FASTA sequences by length to remove sequences below a specified threshold.

License: MIT
Authors