modules/hmmcopy_generatemap

Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.

hmmcopymapcountermappability

https://github.com/nf-core/modules/[...]/modules/nf-core/hmmcopy/generatemap

Description

Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all.

Input

name:type

description

pattern

`meta{:bash}`
`:map`

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

`fasta{:bash}`
`:file`

Input genome fasta file

Output

name:type

description

pattern

`bigwig{:bash}`

`meta{:bash}`
`:map`

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

`*.bw{:bash}`
`:file`

bigwig file containing the mappability of the genome

*.bw

`versions{:bash}`

`versions.yml{:bash}`
`:file`

File containing software versions

versions.yml

Tools

hmmcopy
GPL v3

C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy

github.com/shahcompbio/hmmcopy_utils

modules/hmmcopy_generatemap

Description

Input

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

Output

`bigwig{:bash}`

`meta{:bash}`
`:map`

`*.bw{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

Tools

hmmcopy
GPL v3

maintainers

get in touch

modules/hmmcopy_generatemap

Description

Input

meta{:bash}:map

fasta{:bash}:file

Output

bigwig{:bash}

meta{:bash}:map

*.bw{:bash}:file

versions{:bash}

versions.yml{:bash}:file

Tools

hmmcopy GPL v3

maintainers

get in touch

`meta{:bash}`
`:map`

`fasta{:bash}`
`:file`

`bigwig{:bash}`

`meta{:bash}`
`:map`

`*.bw{:bash}`
`:file`

`versions{:bash}`

`versions.yml{:bash}`
`:file`

hmmcopy
GPL v3