mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
79 lines
2.5 KiB
YAML
79 lines
2.5 KiB
YAML
name: maxbin2
|
|
description: MaxBin is a software that is capable of clustering metagenomic contigs
|
|
keywords:
|
|
- metagenomics
|
|
- assembly
|
|
- binning
|
|
- maxbin2
|
|
- de novo assembly
|
|
- mags
|
|
- metagenome-assembled genomes
|
|
- contigs
|
|
tools:
|
|
- maxbin2:
|
|
description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
|
|
homepage: https://sourceforge.net/projects/maxbin/
|
|
documentation: https://sourceforge.net/projects/maxbin/
|
|
tool_dev_url: https://sourceforge.net/projects/maxbin/
|
|
doi: "10.1093/bioinformatics/btv638"
|
|
licence: ["BSD 3-clause"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- contigs:
|
|
type: file
|
|
description: Multi FASTA file containing assembled contigs of a given sample
|
|
pattern: "*.fasta"
|
|
- reads:
|
|
type: file
|
|
description: Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files.
|
|
pattern: "*.fasta"
|
|
- abund:
|
|
type: file
|
|
description: Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files.
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- binned_fastas:
|
|
type: file
|
|
description: Binned contigs, one per bin designated with numeric IDs
|
|
pattern: "*.fasta.gz"
|
|
- summary:
|
|
type: file
|
|
description: Summary file describing which contigs are being classified into which bin
|
|
pattern: "*.summary"
|
|
- log:
|
|
type: file
|
|
description: Log file recording the core steps of MaxBin algorithm
|
|
pattern: "*.log.gz"
|
|
- marker:
|
|
type: file
|
|
description: Marker gene presence numbers for each bin
|
|
pattern: "*.marker.gz"
|
|
- unbinned_fasta:
|
|
type: file
|
|
description: All sequences that pass the minimum length threshold but are not classified successfully.
|
|
pattern: "*.noclass.gz"
|
|
- tooshort_fasta:
|
|
type: file
|
|
description: All sequences that do not meet the minimum length threshold.
|
|
pattern: "*.tooshort.gz"
|
|
- marker_genes:
|
|
type: file
|
|
description: All sequences that do not meet the minimum length threshold.
|
|
pattern: "*.marker_of_each_gene.tar.gz"
|
|
|
|
authors:
|
|
- "@jfy133"
|