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

`axt_gz`

`meta`
`:map`

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

`*.axt.gz`
`:file`

Gzipped pairwise alignment in Axt (Blastz) format (optional)

*.axt.gz

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Pairwise alignment in BAM format (optional)

*.bam

`bed_gz`

`meta`
`:map`

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

`*.bed.gz`
`:file`

Gzipped pairwise alignment in BED format (optional)

*.bed.gz

`blast_gz`

`meta`
`:map`

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

`*.blast.gz`
`:file`

Gzipped pairwise alignment in blast format (optional)

*.blast.gz

`blasttab_gz`

`meta`
`:map`

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

`*.blasttab.gz`
`:file`

Gzipped pairwise alignment in blasttab format (optional)

*.blasttab.gz

`chain_gz`

`meta`
`:map`

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

`*.chain.gz`
`:file`

Gzipped pairwise alignment in UCSC chain format (optional)

*.chain.gz

`cram`

`meta`
`:map`

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

`*.cram`
`:file`

Pairwise alignment in CRAM format (optional)

*.cram

`gff_gz`

`meta`
`:map`

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

`*.gff.gz`
`:file`

Gzipped pairwise alignment in GFF format (optional)

*.gff.gz

`html_gz`

`meta`
`:map`

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

`*.html.gz`
`:file`

Gzipped pairwise alignment in HTML format (optional)

*.html.gz

`psl_gz`

`meta`
`:map`

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

`*.psl.gz`
`:file`

Gzipped pairwise alignment in PSL (BLAT) format (optional)

*.psl.gz

`sam_gz`

`meta`
`:map`

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

`*.sam.gz`
`:file`

Gzipped pairwise alignment in SAM format (optional)

*.sam.gz

`tab_gz`

`meta`
`:map`

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

`*.tab.gz`
`:file`

Gzipped pairwise alignment in TAB format (optional)

*.tab.gz

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

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

axt_gz

meta:map

*.axt.gz:file

bam

meta:map

*.bam:file

bed_gz

meta:map

*.bed.gz:file

blast_gz

meta:map

*.blast.gz:file

blasttab_gz

meta:map

*.blasttab.gz:file

chain_gz

meta:map

*.chain.gz:file

cram

meta:map

*.cram:file

gff_gz

meta:map

*.gff.gz:file

html_gz

meta:map

*.html.gz:file

psl_gz

meta:map

*.psl.gz:file

sam_gz

meta:map

*.sam.gz:file

tab_gz

meta:map

*.tab.gz:file

versions

versions.yml:file

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`

`axt_gz`

`meta`
`:map`

`*.axt.gz`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`bed_gz`

`meta`
`:map`

`*.bed.gz`
`:file`

`blast_gz`

`meta`
`:map`

`*.blast.gz`
`:file`

`blasttab_gz`

`meta`
`:map`

`*.blasttab.gz`
`:file`

`chain_gz`

`meta`
`:map`

`*.chain.gz`
`:file`

`cram`

`meta`
`:map`

`*.cram`
`:file`

`gff_gz`

`meta`
`:map`

`*.gff.gz`
`:file`

`html_gz`

`meta`
`:map`

`*.html.gz`
`:file`

`psl_gz`

`meta`
`:map`

`*.psl.gz`
`:file`

`sam_gz`

`meta`
`:map`

`*.sam.gz`
`:file`

`tab_gz`

`meta`
`:map`

`*.tab.gz`
`:file`

`versions`

`versions.yml`
`:file`

last
GPL v3-or-later