modules/last_mafconvert

Converts MAF alignments in another format.

LASTconvertalignmentMAF

https://github.com/nf-core/modules/[...]/modules/nf-core/last/mafconvert

Description

Converts MAF alignments in another format.

Input

name:type

description

pattern

`meta`
`:map`

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

`maf`
`:file`

Multiple Alignment Format (MAF) file, optionally compressed with gzip

*.{maf.gz,maf}

`format`
`:string`

Output format (one of axt, bam, blast, blasttab, cram, chain, gff, html, psl, sam, or tab)

`meta2`
`:map`

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

`fasta`
`:file`

Genome file in FASTA format for CRAM conversion. If compressed it must be done in BGZF format (like with the bgzip tool).

*.{fasta,fasta.gz,fasta.bgz,fasta.bgzf}

`meta3`
`:map`

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

`fai`
`:file`

Genome index file needed for CRAM conversion.

*.fai

`meta4`
`:map`

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

`gzi`
`:file`

Genome index file needed for CRAM conversion when the genome file was compressed with the BGZF algorithm.

*.gzi

`meta5`
`:map`

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

`dict`
`:file`

Samtools dictionary of the genome file.

*.dict

Output

name:type

description

pattern

`alignment`

`meta`
`:map`

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

`*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}`
`:file`

Pairwise alignment exported to Axt, BAM, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format.

*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}

`versions_last`

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

The name of the process

`last`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`last`
`:string`

The name of the tool

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

The expression to obtain the version of the tool

Tools

last
GPL v3-or-later

LAST finds & aligns related regions of sequences.

gitlab.com/mcfrith/last gitlab.com/mcfrith/last/-/blob/main/doc https://gitlab.com/mcfrith/last

modules/last_mafconvert

Description

Input

`meta`
`:map`

`maf`
`:file`

`format`
`:string`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`meta5`
`:map`

`dict`
`:file`

Output

`alignment`

`meta`
`:map`

`*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}`
`:file`

`versions_last`

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

`last`
`:string`

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

Topics

`versions`

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

`last`
`:string`

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

Tools

last
GPL v3-or-later

included in

maintainer

get in touch

modules/last_mafconvert

Description

Input

meta:map

maf:file

format:string

meta2:map

fasta:file

meta3:map

fai:file

meta4:map

gzi:file

meta5:map

dict:file

Output

alignment

meta:map

*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}:file

versions_last

${task.process}:string

last:string

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

Topics

versions

${task.process}:string

last:string

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

Tools

last GPL v3-or-later

included in

maintainer

get in touch

`meta`
`:map`

`maf`
`:file`

`format`
`:string`

`meta2`
`:map`

`fasta`
`:file`

`meta3`
`:map`

`fai`
`:file`

`meta4`
`:map`

`gzi`
`:file`

`meta5`
`:map`

`dict`
`:file`

`alignment`

`meta`
`:map`

`*.{axt.gz,bam,bed.gz,blast.gz,blasttab.gz,chain.gz,cram,gff.gz,html.gz,psl.gz,sam.gz,tab.gz}`
`:file`

`versions_last`

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

`last`
`:string`

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

`versions`

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

`last`
`:string`

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

last
GPL v3-or-later