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}

`fai`
`:file`

Genome index file needed for CRAM conversion.

*.fai

`gzi`
`:file`

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

*.gzi

`sizes`
`:file`

File listing sequence names and lenghts in that genome

*.sizes

`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,bcf,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, BCF, BED, BLAST, Chain, CRAM, GFF, HTML PSL, SAM or Tab format. For BCF generation, pass options to bcftools merge with task.ext.args3 and to bcftools call via task.ext.args4.

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

`index`

`meta`
`:map`

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

`*.{bai,crai,csi}`
`:file`

Optional index for the BAM, BCF or CRAM files. Pass --write-index to samtools via task.ext.args2, or BAM and CRAM, and to bcftools call via task.ext.arg4 for BCF.

*.{bai,crai,csi}

`stats`

`meta`
`:map`

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

`*.stats`
`:file`

Statistics on the BCF files.

*.stats

`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`

`fai`
`:file`

`gzi`
`:file`

`sizes`
`:file`

`dict`
`:file`

Output

`alignment`

`meta`
`:map`

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

`index`

`meta`
`:map`

`*.{bai,crai,csi}`
`:file`

`stats`

`meta`
`:map`

`*.stats`
`: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

fai:file

gzi:file

sizes:file

dict:file

Output

alignment

meta:map

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

index

meta:map

*.{bai,crai,csi}:file

stats

meta:map

*.stats: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`

`fai`
`:file`

`gzi`
`:file`

`sizes`
`:file`

`dict`
`:file`

`alignment`

`meta`
`:map`

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

`index`

`meta`
`:map`

`*.{bai,crai,csi}`
`:file`

`stats`

`meta`
`:map`

`*.stats`
`: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