modules/mirtop_gff

mirtop gff generates the GFF3 adapter format to capture miRNA variations

mirnaisomirgff

https://github.com/nf-core/modules/[...]/modules/nf-core/mirtop/gff

Description

mirtop gff generates the GFF3 adapter format to capture miRNA variations

Input

name:type

description

pattern

`meta`
`:map`

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

`bam`
`:file`

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

`meta2`
`:map`

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

`hairpin`
`:file`

Hairpin file

*.{fa,fasta}

`meta3`
`:map`

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

`gtf`
`:file`

GTF file

*.{gtf}

`species`
`:string`

Species name of the GTF file

Output

name:type

description

pattern

`gff`

`meta`
`:map`

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

`mirtop/*mirtop.gff`
`:file`

GFF file

*.{gff}

`versions_mirtop`

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

The name of the process

`mirtop`
`:string`

The name of the tool

`mirtop --version 2>&1 | sed -n 's/^mirtop //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

`mirtop`
`:string`

The name of the tool

`mirtop --version 2>&1 | sed -n 's/^mirtop //p'`
`:eval`

The expression to obtain the version of the tool

Tools

mirtop
MIT License

Small RNA-seq annotation

github.com/miRTop/mirtop mirtop.readthedocs.io/en/latest https://github.com/miRTop/mirtop

modules/mirtop_gff

Description

Input

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`hairpin`
`:file`

`meta3`
`:map`

`gtf`
`:file`

`species`
`:string`

Output

`gff`

`meta`
`:map`

`mirtop/*mirtop.gff`
`:file`

`versions_mirtop`

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

`mirtop`
`:string`

`mirtop --version 2>&1 | sed -n 's/^mirtop //p'`
`:eval`

Topics

`versions`

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

`mirtop`
`:string`

`mirtop --version 2>&1 | sed -n 's/^mirtop //p'`
`:eval`

Tools

mirtop
MIT License

included in

maintainers

get in touch

modules/mirtop_gff

Description

Input

meta:map

bam:file

meta2:map

hairpin:file

meta3:map

gtf:file

species:string

Output

gff

meta:map

mirtop/*mirtop.gff:file

versions_mirtop

${task.process}:string

mirtop:string

mirtop --version 2>&1 | sed -n 's/^mirtop //p':eval

Topics

versions

${task.process}:string

mirtop:string

mirtop --version 2>&1 | sed -n 's/^mirtop //p':eval

Tools

mirtop MIT License

included in

maintainers

get in touch

`meta`
`:map`

`bam`
`:file`

`meta2`
`:map`

`hairpin`
`:file`

`meta3`
`:map`

`gtf`
`:file`

`species`
`:string`

`gff`

`meta`
`:map`

`mirtop/*mirtop.gff`
`:file`

`versions_mirtop`

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

`mirtop`
`:string`

`mirtop --version 2>&1 | sed -n 's/^mirtop //p'`
`:eval`

`versions`

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

`mirtop`
`:string`

`mirtop --version 2>&1 | sed -n 's/^mirtop //p'`
`:eval`

mirtop
MIT License