Description

Find all soft-masked regions in a Fasta file and print their coordinates in BED format

Input

Name
Description
Pattern

meta (map)

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

fasta (file)

Soft-masked Fasta file

*.{fa,fasta}(.gz)?

Output

Name
Description
Pattern

bed

meta (map)

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

*.bed (file)

BED file of all soft-masked regions

*.bed

versions_seqtk

${task.process} (string)

The name of the process

seqtk (string)

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p' (eval)

The expression to obtain the version of the tool

versions_softmask2bed

${task.process} (string)

The name of the process

softmask2bed (string)

The name of the tool

echo 1.0 (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

softmask2bed (string)

The name of the tool

echo 1.0 (eval)

The expression to obtain the version of the tool

${task.process} (string)

The name of the process

seqtk (string)

The name of the tool

seqtk 2>&1 | sed -n 's/^Version: //p' (eval)

The expression to obtain the version of the tool

Tools

seqtk Documentation

Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files.

https://github.com/lh3/seqtkLicense: MIT
Authors