Nextflow Registry | nf-core/metator/pipeline@0.0.0-945dd56

nf-core/metator/pipeline @ 0.0.0-945dd56

Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets.

hic binning metagenomics

Latest version: 0.0.0-945dd56

Total downloads: 4

Source: nf-core/modules

Authors: @prototaxites

Maintainers: @prototaxites

Summary

Metagenomic Tridimensional Organisation-based Reassembly - A set of scripts that streamlines the processing and binning of metagenomic metaHiC datasets.

Get started

Add the following snippet to your workflow script to include this module.

include { METATOR_PIPELINE } from 'nf-core/metator/pipeline'

License

MIT License

Process

`Name`	`METATOR_PIPELINE`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`contigs` file	Reference assembly to bin, in FASTA format `*.{fa,fa.gz}`
`hic_input` file	One of: a list of two PE read FASTQ files ([R1, R2]) a list of two BAM files ([R1, R2]), with forward and reverse reads mapped independently to the reference a single pairs file `*.{fastq,fastq.gz,fq,fq.gz,bam,pairs,pairs.gz}`
`depths` file	(optional) A TSV file describing the coverages of each input contig, as created by jgi_summarize_bam_contig_depths `*.{txt,tsv}`

Output 9 channels

#1 bins tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`final_bin_unscaffold/*.fa.gz` file	Output bins `*.fa.gz`

#2 plots tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`plot/*.png` file	Plots summarising binning process `*.png`

#3 network tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`network.txt` file	TSV describing Hi-C network `network.txt`

#4 contig2bin tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`binning.txt` file	Contig-to-bin mapping for bins `binning.txt`

#5 bin_summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`bin_summary.txt` file	Summary TSV of bins `bin_summary.txt`

#6 contig_data tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`contig_data_final.txt` file	TSV describing input contigs `contig_data_final.txt`

#7 versions_find tuple

`${task.process}` string	The name of the process
`find` string	The name of the tool
`find --version \| sed '1!d; s/.* //'` eval	The expression to obtain the version of the tool

#8 versions_gunzip tuple

`${task.process}` string	The name of the process
`gunzip` string	The name of the tool
`gunzip --version \|& sed "1!d;s/^.(gzip) //;s/ Copyright.//"` eval	The expression to obtain the version of the tool

#9 versions_metator tuple

`${task.process}` string	The name of the process
`metator` string	The name of the tool
`metator -v` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
metator	Metagenomic binning based on Hi-C data.