modules/concoct_concoct

Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples

contigsfragmentmagsbinningconcoctkmernucleotide compositionmetagenomicsbins

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

Description

Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples

Input

name:type

description

pattern

`meta`
`:map`

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

`coverage_file`
`:file`

Subcontig coverage TSV table (typically generated with concoct_coverage_table.py)

*.tsv

`fasta`
`:file`

FASTA file containing subcontigs (typically generated with cutup_fasta.py)

*.fasta

Output

name:type

description

pattern

`args_txt`

`meta`
`:map`

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

`*_args.txt`
`:file`

File containing execution parameters

*_args.txt

`clustering_csv`

`meta`
`:map`

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

`*_clustering_gt1000.csv`
`:file`

CSV containing information which subcontig is assigned to which cluster

*_clustering_gt1000.csv

`log_txt`

`meta`
`:map`

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

`*_log.txt`
`:file`

Log file of tool execution

*_log.txt

`original_data_csv`

`meta`
`:map`

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

`*_original_data_gt1000.csv`
`:file`

Original CONCOCT GT1000 output

*_original_data_gt1000.csv

`pca_components_csv`

`meta`
`:map`

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

`*_PCA_components_data_gt1000.csv`
`:file`

Untransformed PCA component values

*_PCA_components_data_gt1000.csv

`pca_transformed_csv`

`meta`
`:map`

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

`*_PCA_transformed_data_gt1000.csv`
`:file`

Transformed PCA component values

*_PCA_transformed_data_gt1000.csv

`versions`

`versions.yml`
`:file`

File containing software versions

versions.yml

Tools

concoct
FreeBSD

Clustering cONtigs with COverage and ComposiTion

concoct.readthedocs.io/en/latest https://github.com/BinPro/CONCOCT 10.1038/nmeth.3103

modules/concoct_concoct

Description

Input

`meta`
`:map`

`coverage_file`
`:file`

`fasta`
`:file`

Output

`args_txt`

`meta`
`:map`

`*_args.txt`
`:file`

`clustering_csv`

`meta`
`:map`

`*_clustering_gt1000.csv`
`:file`

`log_txt`

`meta`
`:map`

`*_log.txt`
`:file`

`original_data_csv`

`meta`
`:map`

`*_original_data_gt1000.csv`
`:file`

`pca_components_csv`

`meta`
`:map`

`*_PCA_components_data_gt1000.csv`
`:file`

`pca_transformed_csv`

`meta`
`:map`

`*_PCA_transformed_data_gt1000.csv`
`:file`

`versions`

`versions.yml`
`:file`

Tools

concoct
FreeBSD

included in

maintainer

get in touch

modules/concoct_concoct

Description

Input

meta:map

coverage_file:file

fasta:file

Output

args_txt

meta:map

*_args.txt:file

clustering_csv

meta:map

*_clustering_gt1000.csv:file

log_txt

meta:map

*_log.txt:file

original_data_csv

meta:map

*_original_data_gt1000.csv:file

pca_components_csv

meta:map

*_PCA_components_data_gt1000.csv:file

pca_transformed_csv

meta:map

*_PCA_transformed_data_gt1000.csv:file

versions

versions.yml:file

Tools

concoct FreeBSD

included in

maintainer

get in touch

`meta`
`:map`

`coverage_file`
`:file`

`fasta`
`:file`

`args_txt`

`meta`
`:map`

`*_args.txt`
`:file`

`clustering_csv`

`meta`
`:map`

`*_clustering_gt1000.csv`
`:file`

`log_txt`

`meta`
`:map`

`*_log.txt`
`:file`

`original_data_csv`

`meta`
`:map`

`*_original_data_gt1000.csv`
`:file`

`pca_components_csv`

`meta`
`:map`

`*_PCA_components_data_gt1000.csv`
`:file`

`pca_transformed_csv`

`meta`
`:map`

`*_PCA_transformed_data_gt1000.csv`
`:file`

`versions`

`versions.yml`
`:file`

concoct
FreeBSD