modules/ragtag_scaffold

Scaffolding is the process of ordering and orienting draft assembly (query) sequences into longer sequences. Gaps (stretches of “N” characters) are placed between adjacent query sequences to indicate the presence of unknown sequence. RagTag uses whole-genome alignments to a reference assembly to scaffold query sequences. RagTag does not alter input query sequence in any way and only orders and orients sequences, joining them with gaps.

scaffoldingragtagassemblygenome

https://github.com/nf-core/modules/[...]/modules/nf-core/ragtag/scaffold

Description

Input

name:type

description

pattern

`meta`
`:map`

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

`assembly`
`:file`

Assembly to be scaffolded

*.{fasta,fasta.gz,fa,fa.gz}

`meta2`
`:map`

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

`reference`
`:file`

Reference assembly

*.{fasta,fasta.gz,fa,fa.gz}

`meta3`
`:map`

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

`exclude`
`:file`

list of target sequences to ignore

*.txt

`meta4`
`:map`

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

`skip`
`:file`

list of query sequences to leave unplaced

*.txt

`hard_skip`
`:file`

list of query headers to leave unplaced and exclude from ‘chr0’ (‘-C’)

*.txt

Output

name:type

description

pattern

`corrected_assembly`

`meta`
`:map`

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

`*.fasta.gz`
`:file`

FASTA file containing the patched assembly

*.fasta.gz

`corrected_agp`

`meta`
`:map`

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

`*.agp`
`:file`

agp file defining how corrected_assembly is built

*.agp

`corrected_stats`

`meta`
`:map`

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

`*.stats`
`:file`

Statistics on the scaffold

*.stats

`ragtag_paf`

`meta`
`:map`

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

`*.paf.gz`
`:file`

PAF file of alignments between reference and input

*.paf.gz

`ragtag_paf_log`

`meta`
`:map`

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

`*.paf.log`
`:file`

Log file of the ragtag alignment when using minimap2

*.paf.log

`ragtag_delta`

`meta`
`:map`

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

`*.delta.gz`
`:file`

Nucmer delta file of alignments between reference and input

*.delta.gz

`ragtag_delta_log`

`meta`
`:map`

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

`*.delta.log`
`:file`

Log file of the ragtag alignment when using nucmer

*.paf.log

`confidence_txt`

`meta`
`:map`

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

`*.confidence.txt`
`:file`

Confidence scores used in scaffolding

*.confidence.txt

`versions_ragtag`

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

The name of the process

`ragtag`
`:string`

The name of the tool

`ragtag.py -v | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`ragtag`
`:string`

The name of the tool

`ragtag.py -v | sed 's/v//'`
`:eval`

The expression to obtain the version of the tool

Tools

ragtag
MIT

Fast reference-guided genome assembly scaffolding

github.com/malonge/RagTag/wiki https://github.com/malonge/RagTag 10.1186/s13059-022-02823-7

modules/ragtag_scaffold

Description

Input

meta :map

assembly :file

meta2 :map

reference :file

meta3 :map

exclude :file

meta4 :map

skip :file

hard_skip :file

Output

corrected_assembly

meta :map

*.fasta.gz :file

corrected_agp

meta :map

*.agp :file

corrected_stats

meta :map

*.stats :file

ragtag_paf

meta :map

*.paf.gz :file

ragtag_paf_log

meta :map

*.paf.log :file

ragtag_delta

meta :map

*.delta.gz :file

ragtag_delta_log

meta :map

*.delta.log :file

confidence_txt

meta :map

*.confidence.txt :file

versions_ragtag

${task.process} :string

ragtag :string

ragtag.py -v | sed 's/v//' :eval

Topics

versions

${task.process} :string

ragtag :string

ragtag.py -v | sed 's/v//' :eval

Tools

ragtagMIT

included in

maintainer

get in touch

`meta`
`:map`

`assembly`
`:file`

`meta2`
`:map`

`reference`
`:file`

`meta3`
`:map`

`exclude`
`:file`

`meta4`
`:map`

`skip`
`:file`

`hard_skip`
`:file`

`corrected_assembly`

`meta`
`:map`

`*.fasta.gz`
`:file`

`corrected_agp`

`meta`
`:map`

`*.agp`
`:file`

`corrected_stats`

`meta`
`:map`

`*.stats`
`:file`

`ragtag_paf`

`meta`
`:map`

`*.paf.gz`
`:file`

`ragtag_paf_log`

`meta`
`:map`

`*.paf.log`
`:file`

`ragtag_delta`

`meta`
`:map`

`*.delta.gz`
`:file`

`ragtag_delta_log`

`meta`
`:map`

`*.delta.log`
`:file`

`confidence_txt`

`meta`
`:map`

`*.confidence.txt`
`:file`

`versions_ragtag`

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

`ragtag`
`:string`

`ragtag.py -v | sed 's/v//'`
`:eval`

`versions`

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

`ragtag`
`:string`

`ragtag.py -v | sed 's/v//'`
`:eval`

ragtag
MIT