Description

Remove all soft-masking from a Fasta file by turning all lower-case sequence characters to upper case.

Input

Name
Description
Pattern

meta (map)

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

fasta (file)

Fasta file, possibly compressed

*.fa(sta)?(.gz)?

Output

Name
Description
Pattern

unmasked

meta (map)

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

*.unmasked.fa (file)

Unmasked FASTA file

*.unmasked.fa

versions_gawk

${task.process} (string)

The name of the process

gawk (string)

The name of the tool

gawk --version | grep -o -E "[0-9]+(.[0-9]+)+" | head -n1 (eval)

The expression to obtain the version of the tool

versions_unmask

${task.process} (string)

The name of the process

unmask (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

unmask (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

gawk (string)

The name of the tool

gawk --version | grep -o -E "[0-9]+(.[0-9]+)+" | head -n1 (eval)

The expression to obtain the version of the tool

Tools

Authors