modules/ultra_align

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome

uLTRAalignminimap2long_readisoseqont

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

Description

uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

A fasta or fastq file of reads to align

*.{fa,fasta,fastq}

`meta2`
`:map`

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

`genome`
`:file`

A fasta file of reference genome

*.{fa,fasta}

`meta3`
`:map`

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

`pickle`
`:file`

Pickle files generated by uLTRA index

*.pickle

`db`
`:file`

Database generated by uLTRA index

*.db

Output

name:type

description

pattern

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

The aligned reads in bam format

*.bam

`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_samtools`

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

The name of the process

`samtools`
`:string`

The name of the tool

`samtools --version | sed -n '1s/samtools //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

`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

`samtools`
`:string`

The name of the tool

`samtools --version | sed -n '1s/samtools //p'`
`: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_align

Description

Input

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`genome`
`:file`

`meta3`
`:map`

`pickle`
`:file`

`db`
`:file`

Output

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_ultra`

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

`ultra`
`:string`

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

`versions_samtools`

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

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

Topics

`versions`

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

`ultra`
`:string`

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

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

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

Tools

ultra
GNU GPLV3

included in

maintainer

get in touch

modules/ultra_align

Description

Input

meta :map

reads :file

meta2 :map

genome :file

meta3 :map

pickle :file

db :file

Output

bam

meta :map

*.bam :file

versions_ultra

${task.process} :string

ultra :string

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

versions_samtools

${task.process} :string

samtools :string

samtools --version | sed -n '1s/samtools //p' :eval

Topics

versions

${task.process} :string

ultra :string

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

${task.process} :string

samtools :string

samtools --version | sed -n '1s/samtools //p' :eval

Tools

ultraGNU GPLV3

included in

maintainer

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`genome`
`:file`

`meta3`
`:map`

`pickle`
`:file`

`db`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`versions_ultra`

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

`ultra`
`:string`

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

`versions_samtools`

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

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

`versions`

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

`ultra`
`:string`

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

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

`samtools`
`:string`

`samtools --version | sed -n '1s/samtools //p'`
`:eval`

ultra
GNU GPLV3