modules/gstama_polyacleanup

Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)

gstamagstama/polyacleanuplong-readisoseqtamatrancriptomeannotation

https://github.com/nf-core/modules/[...]/modules/nf-core/gstama/polyacleanup

Description

Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3)

Input

name:type

description

pattern

`meta`
`:map`

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

`fasta`
`:file`

Full Length Non Chimeric reads in fasta format

*.{fa,fasta}

Output

name:type

description

pattern

`fasta`

`meta`
`:map`

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

`*.fa.gz`
`:file`

The Full Length Non Chimeric reads cleaned from remaining polyA tails. The sequences are in FASTA format compressed with gzip.

*.fa.gz

`report`

`meta`
`:map`

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

`*_polya_flnc_report.txt.gz`
`:file`

A text file describing the number of polyA tails removed and their length. Compressed with gzip.

*_polya_flnc_report.txt.gz

`tails`

`meta`
`:map`

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

`*_tails.fa.gz`
`:file`

A gzip compressed FASTA file of trimmed polyA tails.

*_tails.fa.gz

`versions_gstama`

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

The name of the process

`gstama`
`:string`

The name of the tool

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`gstama`
`:string`

The name of the tool

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

The expression to obtain the version of the tool

Tools

gstama
GPL v3 License

Gene-Switch Transcriptome Annotation by Modular Algorithms

github.com/sguizard/gs-tama github.com/GenomeRIK/tama/wiki https://github.com/sguizard/gs-tama 10.1186/s12864-020-07123-7

modules/gstama_polyacleanup

Description

Input

`meta`
`:map`

`fasta`
`:file`

Output

`fasta`

`meta`
`:map`

`*.fa.gz`
`:file`

`report`

`meta`
`:map`

`*_polya_flnc_report.txt.gz`
`:file`

`tails`

`meta`
`:map`

`*_tails.fa.gz`
`:file`

`versions_gstama`

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

`gstama`
`:string`

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

Topics

`versions`

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

`gstama`
`:string`

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

Tools

gstama
GPL v3 License

included in

maintainer

get in touch

modules/gstama_polyacleanup

Description

Input

meta:map

fasta:file

Output

fasta

meta:map

*.fa.gz:file

report

meta:map

*_polya_flnc_report.txt.gz:file

tails

meta:map

*_tails.fa.gz:file

versions_gstama

${task.process}:string

gstama:string

tama_collapse.py -version | sed -n 's/tc_version_date_//p':eval

Topics

versions

${task.process}:string

gstama:string

tama_collapse.py -version | sed -n 's/tc_version_date_//p':eval

Tools

gstama GPL v3 License

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`fasta`

`meta`
`:map`

`*.fa.gz`
`:file`

`report`

`meta`
`:map`

`*_polya_flnc_report.txt.gz`
`:file`

`tails`

`meta`
`:map`

`*_tails.fa.gz`
`:file`

`versions_gstama`

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

`gstama`
`:string`

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

`versions`

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

`gstama`
`:string`

`tama_collapse.py -version | sed -n 's/tc_version_date_//p'`
`:eval`

gstama
GPL v3 License