modules/segemehl_align

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

alignmentcircrnasplicingfusions

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

Description

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

FASTA or FASTQ files

*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}

`meta2`
`:map`

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

`fasta`
`:file`

Reference genome FASTA file used to construct Segemehl

*.{fa,fasta}

`index`
`:file`

Segemehl Index file from SEGEMEHL_INDEX

*.idx

Output

name:type

description

pattern

`alignment`

`meta`
`:map`

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

`${prefix}/${prefix}.${suffix}`
`:file`

File containing genomic alignments in SAM format (please add “-b” flag to task.ext.args for BAM)

*.{sam,bam}

`trans_alignments`

`meta`
`:map`

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

`${prefix}/${prefix}.trns.txt`
`:file`

Custom text file containing all single split alignments predicted to be in trans (optional, only if -S flag is set in task.ext.args)

*.trns.txt

`multi_bed`

`meta`
`:map`

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

`${prefix}/${prefix}.mult.bed`
`:file`

Bed file containing all splice events predicted in the split read alignments. (optional, only if -S flag is set in task.ext.args)

*.mult.bed

`single_bed`

`meta`
`:map`

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

`${prefix}/${prefix}.sngl.bed`
`:file`

Bed file containing all single splice events predicted in the split read alignments. (optional, only if -S flag is set in task.ext.args)

*.sngl.bed

`versions_segemehl`

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

The name of the process

`segemehl`
`:string`

The name of the tool

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`segemehl`
`:string`

The name of the tool

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

The expression to obtain the version of the tool

Tools

segemehl
GPL v3

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

bioinf.uni-leipzig.de/Software/segemehl 10.1186/gb-2014-15-2-r34

modules/segemehl_align

Description

Input

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

Output

`alignment`

`meta`
`:map`

`${prefix}/${prefix}.${suffix}`
`:file`

`trans_alignments`

`meta`
`:map`

`${prefix}/${prefix}.trns.txt`
`:file`

`multi_bed`

`meta`
`:map`

`${prefix}/${prefix}.mult.bed`
`:file`

`single_bed`

`meta`
`:map`

`${prefix}/${prefix}.sngl.bed`
`:file`

`versions_segemehl`

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

`segemehl`
`:string`

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

Topics

`versions`

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

`segemehl`
`:string`

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

Tools

segemehl
GPL v3

included in

maintainer

get in touch

modules/segemehl_align

Description

Input

meta :map

reads :file

meta2 :map

fasta :file

index :file

Output

alignment

meta :map

${prefix}/${prefix}.${suffix} :file

trans_alignments

meta :map

${prefix}/${prefix}.trns.txt :file

multi_bed

meta :map

${prefix}/${prefix}.mult.bed :file

single_bed

meta :map

${prefix}/${prefix}.sngl.bed :file

versions_segemehl

${task.process} :string

segemehl :string

segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]*/!d;s/^ //;s/ .*//' :eval

Topics

versions

${task.process} :string

segemehl :string

segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]*/!d;s/^ //;s/ .*//' :eval

Tools

segemehlGPL v3

included in

maintainer

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`fasta`
`:file`

`index`
`:file`

`alignment`

`meta`
`:map`

`${prefix}/${prefix}.${suffix}`
`:file`

`trans_alignments`

`meta`
`:map`

`${prefix}/${prefix}.trns.txt`
`:file`

`multi_bed`

`meta`
`:map`

`${prefix}/${prefix}.mult.bed`
`:file`

`single_bed`

`meta`
`:map`

`${prefix}/${prefix}.sngl.bed`
`:file`

`versions_segemehl`

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

`segemehl`
`:string`

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

`versions`

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

`segemehl`
`:string`

`segemehl.x 2>&1 | sed '/^ [0-9]\.[0-9\.]/!d;s/^ //;s/ .//'`
`:eval`

segemehl
GPL v3