modules/myloasm

Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command.

assemblymetagenomelong-readpacbionanopore

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

Description

Myloasm is a de novo metagenome assembler for long-read sequencing data. It takes sequencing reads and outputs polished contigs in a single command.

Input

name:type

description

pattern

`meta`
`:map`

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

`reads`
`:file`

Input long reads in FASTQ or FASTA format (FASTQ preferred for base quality information)

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

Output

name:type

description

pattern

`results`

`meta`
`:map`

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

`${prefix}`
`:directory`

Directory containing all myloasm output files and folders

*

`contigs`

`meta`
`:map`

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

`${prefix}/${prefix}.assembly_primary.fa.gz`
`:file`

Primary assembly contigs in FASTA format

${prefix}.assembly_primary.fa.gz

`gfa`

`meta`
`:map`

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

`${prefix}/${prefix}.final_contig_graph.gfa.gz`
`:file`

Final contig graph in GFA format

${prefix}.final_contig_graph.gfa.gz

`contigs_alt`

`meta`
`:map`

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

`${prefix}/alternate_assemblies/${prefix}.assembly_alternate.fa.gz`
`:file`

Alternative assembly contigs in FASTA format

${prefix}.assembly_alternate.fa.gz

`contigs_dup`

`meta`
`:map`

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

`${prefix}/alternate_assemblies/${prefix}.duplicated_contigs.fa.gz`
`:file`

Duplicated contigs in FASTA format

${prefix}.duplicated_contigs.fa.gz

`mapping`

`meta`
`:map`

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

`${prefix}/3-mapping/${prefix}.map_to_unitigs.paf.gz`
`:file`

Mapping of reads to unitigs in PAF format (compressed)

${prefix}.map_to_unitigs.paf.gz

`log`

`meta`
`:map`

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

`${prefix}/*.log`
`:file`

MyloAsm log files containing assembly process information

*.log

`versions_myloasm`

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

The name of the process

`myloasm`
`:string`

The name of the tool

`myloasm --version | sed 's/.* //'`
`:eval`

The expression used to obtain the version of the tool

Topics

name:type

description

pattern

`versions`

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

The name of the process

`myloasm`
`:string`

The name of the tool

`myloasm --version | sed 's/.* //'`
`:eval`

The expression used to obtain the version of the tool

Tools

myloasm
MIT

Myloasm is a long-read assembler for metagenomes

myloasm-docs.github.io https://github.com/bluenote-1577/myloasm/tree/main 10.1101/2025.09.05.674543

modules/myloasm

Description

Input

`meta`
`:map`

`reads`
`:file`

Output

`results`

`meta`
`:map`

`${prefix}`
`:directory`

`contigs`

`meta`
`:map`

`${prefix}/${prefix}.assembly_primary.fa.gz`
`:file`

`gfa`

`meta`
`:map`

`${prefix}/${prefix}.final_contig_graph.gfa.gz`
`:file`

`contigs_alt`

`meta`
`:map`

`${prefix}/alternate_assemblies/${prefix}.assembly_alternate.fa.gz`
`:file`

`contigs_dup`

`meta`
`:map`

`${prefix}/alternate_assemblies/${prefix}.duplicated_contigs.fa.gz`
`:file`

`mapping`

`meta`
`:map`

`${prefix}/3-mapping/${prefix}.map_to_unitigs.paf.gz`
`:file`

`log`

`meta`
`:map`

`${prefix}/*.log`
`:file`

`versions_myloasm`

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

`myloasm`
`:string`

`myloasm --version | sed 's/.* //'`
`:eval`

Topics

`versions`

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

`myloasm`
`:string`

`myloasm --version | sed 's/.* //'`
`:eval`

Tools

myloasm
MIT

maintainer

get in touch

modules/myloasm

Description

Input

meta :map

reads :file

Output

results

meta :map

${prefix} :directory

contigs

meta :map

${prefix}/${prefix}.assembly_primary.fa.gz :file

gfa

meta :map

${prefix}/${prefix}.final_contig_graph.gfa.gz :file

contigs_alt

meta :map

${prefix}/alternate_assemblies/${prefix}.assembly_alternate.fa.gz :file

contigs_dup

meta :map

${prefix}/alternate_assemblies/${prefix}.duplicated_contigs.fa.gz :file

mapping

meta :map

${prefix}/3-mapping/${prefix}.map_to_unitigs.paf.gz :file

log

meta :map

${prefix}/*.log :file

versions_myloasm

${task.process} :string

myloasm :string

myloasm --version | sed 's/.* //' :eval

Topics

versions

${task.process} :string

myloasm :string

myloasm --version | sed 's/.* //' :eval

Tools

myloasmMIT

maintainer

get in touch

`meta`
`:map`

`reads`
`:file`

`results`

`meta`
`:map`

`${prefix}`
`:directory`

`contigs`

`meta`
`:map`

`${prefix}/${prefix}.assembly_primary.fa.gz`
`:file`

`gfa`

`meta`
`:map`

`${prefix}/${prefix}.final_contig_graph.gfa.gz`
`:file`

`contigs_alt`

`meta`
`:map`

`${prefix}/alternate_assemblies/${prefix}.assembly_alternate.fa.gz`
`:file`

`contigs_dup`

`meta`
`:map`

`${prefix}/alternate_assemblies/${prefix}.duplicated_contigs.fa.gz`
`:file`

`mapping`

`meta`
`:map`

`${prefix}/3-mapping/${prefix}.map_to_unitigs.paf.gz`
`:file`

`log`

`meta`
`:map`

`${prefix}/*.log`
`:file`

`versions_myloasm`

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

`myloasm`
`:string`

`myloasm --version | sed 's/.* //'`
`:eval`

`versions`

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

`myloasm`
`:string`

`myloasm --version | sed 's/.* //'`
`:eval`

myloasm
MIT