modules/tcoffee_tcs

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

alignmentMSAevaluation

https://github.com/nf-core/modules/[...]/modules/nf-core/tcoffee/tcs

Description

Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score.

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, … ]

`msa`
`:file`

fasta file containing the alignment to be evaluated. May be gzipped or uncompressed.

*.{aln,fa,fasta,fas}{.gz,}

`meta2`
`:map`

Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]

`lib`
`:file`

lib file containing the alignment library of the given msa.

*{.tc_lib,*_lib}

Output

name:type

description

pattern

`tcs`

`meta`
`:map`

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

`*.tcs`
`:file`

The msa represented in tcs format, prepended with TCS scores

*.tcs

`scores`

`meta`
`:map`

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

`*.scores`
`:file`

a file containing the score of the alignment in csv format

*.scores

`versions_tcoffee`

`${task.process}`
`:string`

The name of the process

`tcoffee`
`:string`

The name of the tool

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

The expression to obtain the version of the tool

`versions_pigz`

`${task.process}`
`:string`

The name of the process

`pigz`
`:string`

The name of the tool

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

`${task.process}`
`:string`

The name of the process

`tcoffee`
`:string`

The name of the tool

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

The expression to obtain the version of the tool

`${task.process}`
`:string`

The name of the process

`pigz`
`:string`

The name of the tool

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

The expression to obtain the version of the tool

Tools

tcoffee
GPL v3

A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence

http://www.tcoffee.org/Projects/tcoffee tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation https://github.com/cbcrg/tcoffee 10.1006/jmbi.2000.4042

pigz

Parallel implementation of the gzip algorithm.

zlib.net/pigz zlib.net/pigz/pigz.pdf

modules/tcoffee_tcs

Description

Input

`meta`
`:map`

`msa`
`:file`

`meta2`
`:map`

`lib`
`:file`

Output

`tcs`

`meta`
`:map`

`*.tcs`
`:file`

`scores`

`meta`
`:map`

`*.scores`
`:file`

`versions_tcoffee`

`${task.process}`
`:string`

`tcoffee`
`:string`

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

`versions_pigz`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

Topics

`versions`

`${task.process}`
`:string`

`tcoffee`
`:string`

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

Tools

tcoffee
GPL v3

pigz

included in

maintainer

get in touch

modules/tcoffee_tcs

Description

Input

meta:map

msa:file

meta2:map

lib:file

Output

tcs

meta:map

*.tcs:file

scores

meta:map

*.scores:file

versions_tcoffee

${task.process}:string

tcoffee:string

t_coffee -version | awk '{gsub("Version_", ""); print \$3}':eval

versions_pigz

${task.process}:string

pigz:string

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//":eval

Topics

versions

${task.process}:string

tcoffee:string

t_coffee -version | awk '{gsub("Version_", ""); print \$3}':eval

${task.process}:string

pigz:string

pigz --version 2>&1 | sed "s/^.*pigz[[:space:]]*//":eval

Tools

tcoffee GPL v3

pigz

included in

maintainer

get in touch

`meta`
`:map`

`msa`
`:file`

`meta2`
`:map`

`lib`
`:file`

`tcs`

`meta`
`:map`

`*.tcs`
`:file`

`scores`

`meta`
`:map`

`*.scores`
`:file`

`versions_tcoffee`

`${task.process}`
`:string`

`tcoffee`
`:string`

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

`versions_pigz`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

`versions`

`${task.process}`
`:string`

`tcoffee`
`:string`

`t_coffee -version | awk '{gsub("Version_", ""); print \$3}'`
`:eval`

`${task.process}`
`:string`

`pigz`
`:string`

`pigz --version 2>&1 | sed "s/^.pigz[[:space:]]//"`
`:eval`

tcoffee
GPL v3