modules/minimap2_align

A versatile pairwise aligner for genomic and spliced nucleotide sequences

alignfastafastqgenomepafreference

https://github.com/nf-core/modules/[...]/modules/nf-core/minimap2/align

Description

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

List of input FASTA or FASTQ files of size 1 and 2 for single-end and paired-end data, respectively.

`meta2`
`:map`

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

`reference`
`:file`

Reference database in FASTA format.

`bam_format`
`:boolean`

Specify that output should be in BAM format

`bam_index_extension`
`:string`

BAM alignment index extension (e.g. “bai”)

`cigar_paf_format`
`:boolean`

Specify that output CIGAR should be in PAF format

`cigar_bam`
`:boolean`

Write CIGAR with >65535 ops at the CG tag. This is recommended when doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)

Output

name:type

description

pattern

`paf`

`meta`
`:map`

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

`*.paf`
`:file`

Alignment in PAF format

*.paf

`bam`

`meta`
`:map`

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

`*.bam`
`:file`

Alignment in BAM format

*.bam

`index`

`meta`
`:map`

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

`*.bam.${bam_index_extension}`
`:file`

BAM alignment index

*.bam.*

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

minimap2
MIT

A versatile pairwise aligner for genomic and spliced nucleotide sequences.

github.com/lh3/minimap2 github.com/lh3/minimap2#uguide

modules/minimap2_align

Description

Input

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`reference`
`:file`

`bam_format`
`:boolean`

`bam_index_extension`
`:string`

`cigar_paf_format`
`:boolean`

`cigar_bam`
`:boolean`

Output

`paf`

`meta`
`:map`

`*.paf`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`index`

`meta`
`:map`

`*.bam.${bam_index_extension}`
`:file`

`versions`

`versions.yml`
`:file`

Tools

minimap2
MIT

included in

maintainers

get in touch

modules/minimap2_align

Description

Input

meta:map

reads:file

meta2:map

reference:file

bam_format:boolean

bam_index_extension:string

cigar_paf_format:boolean

cigar_bam:boolean

Output

paf

meta:map

*.paf:file

bam

meta:map

*.bam:file

index

meta:map

*.bam.${bam_index_extension}:file

versions

versions.yml:file

Tools

minimap2 MIT

included in

maintainers

get in touch

`meta`
`:map`

`reads`
`:file`

`meta2`
`:map`

`reference`
`:file`

`bam_format`
`:boolean`

`bam_index_extension`
`:string`

`cigar_paf_format`
`:boolean`

`cigar_bam`
`:boolean`

`paf`

`meta`
`:map`

`*.paf`
`:file`

`bam`

`meta`
`:map`

`*.bam`
`:file`

`index`

`meta`
`:map`

`*.bam.${bam_index_extension}`
`:file`

`versions`

`versions.yml`
`:file`

minimap2
MIT