modules/ultra_index

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment

uLTRAindexminimap2long_readisoseqont

https://github.com/nf-core/modules/[...]/modules/nf-core/ultra/index

Description

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment

Input

name:type

description

pattern

`meta`
`:map`

Groovy Map containing genome information e.g. [ id:‘test’ ]

`fasta`
`:file`

A fasta file of the genome to use as reference for mapping

*.{fasta, fa}

`meta2`
`:map`

Groovy Map containing gtf information e.g. [ id:‘test’ ]

`gtf`
`:file`

An annotation file of the reference genome in GTF format

*.gtf

Output

name:type

description

pattern

`database`

`meta`
`:map`

Groovy Map containing genome information e.g. [ id:‘test’ ]

`*.db`
`:file`

Index database

*.db

`pickle`

`meta`
`:map`

Groovy Map containing genome information e.g. [ id:‘test’ ]

`*.pickle`
`:file`

Index file

*.pickle

`versions_ultra`

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

The name of the process

`ultra`
`:string`

The name of the tool

`uLTRA --version | sed 's/uLTRA //'`
`:eval`

The expression to obtain the version of the tool

`versions_gffutils`

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

The name of the process

`gffutils`
`:string`

The name of the tool

`python -c 'import gffutils; print(gffutils.version)'`
`:eval`

The expression to obtain the version of the tool

`versions_sqlite`

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

The name of the process

`sqlite`
`:string`

The name of the tool

`python -c 'import sqlite3; print(sqlite3.sqlite_version)'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`ultra`
`:string`

The name of the tool

`uLTRA --version | sed 's/uLTRA //'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`gffutils`
`:string`

The name of the tool

`python -c 'import gffutils; print(gffutils.version)'`
`:eval`

The expression to obtain the version of the tool

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

The name of the process

`sqlite`
`:string`

The name of the tool

`python -c 'import sqlite3; print(sqlite3.sqlite_version)'`
`:eval`

The expression to obtain the version of the tool

Tools

ultra
GNU GPLV3

Splice aligner of long transcriptomic reads to genome.

github.com/ksahlin/uLTRA 10.1093/bioinformatics/btab540

modules/ultra_index

Description

Input

meta :map

fasta :file

meta2 :map

gtf :file

Output

database

meta :map

*.db :file

pickle

meta :map

*.pickle :file

versions_ultra

${task.process} :string

ultra :string

uLTRA --version | sed 's/uLTRA //' :eval

versions_gffutils

${task.process} :string

gffutils :string

python -c 'import gffutils; print(gffutils.__version__)' :eval

versions_sqlite

${task.process} :string

sqlite :string

python -c 'import sqlite3; print(sqlite3.sqlite_version)' :eval

Topics

versions

${task.process} :string

ultra :string

uLTRA --version | sed 's/uLTRA //' :eval

${task.process} :string

gffutils :string

python -c 'import gffutils; print(gffutils.__version__)' :eval

${task.process} :string

sqlite :string

python -c 'import sqlite3; print(sqlite3.sqlite_version)' :eval

Tools

ultraGNU GPLV3

included in

maintainer

get in touch

`meta`
`:map`

`fasta`
`:file`

`meta2`
`:map`

`gtf`
`:file`

`database`

`meta`
`:map`

`*.db`
`:file`

`pickle`

`meta`
`:map`

`*.pickle`
`:file`

`versions_ultra`

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

`ultra`
`:string`

`uLTRA --version | sed 's/uLTRA //'`
`:eval`

`versions_gffutils`

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

`gffutils`
`:string`

`python -c 'import gffutils; print(gffutils.version)'`
`:eval`

`versions_sqlite`

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

`sqlite`
`:string`

`python -c 'import sqlite3; print(sqlite3.sqlite_version)'`
`:eval`

`versions`

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

`ultra`
`:string`

`uLTRA --version | sed 's/uLTRA //'`
`:eval`

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

`gffutils`
`:string`

`python -c 'import gffutils; print(gffutils.version)'`
`:eval`

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

`sqlite`
`:string`

`python -c 'import sqlite3; print(sqlite3.sqlite_version)'`
`:eval`

ultra
GNU GPLV3