fasta_binning_concoct

Runs the CONCOCT workflow of contig binning

concoctbinningmetagenomicscontigs

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

Description

Runs the CONCOCT workflow of contig binning

Input

name

description

pattern

`ch_fasta`

Structure: [ val(meta), path(fasta)]
File containing raw assembled contigs in FASTA format.

`ch_bam`

Structure: [ val(meta), path(bam), path(bai)]
BAM and associated index files file representing reads mapped against each
contig in ch_fasta. Meta must be identical between ch_fasta and ch_bam entries.

Output

name

description

pattern

`coverage_table`

Structure: [ val(meta), path(tsv)]
(Sub)contig coverage table

`original_csv`

Structure: [ val(meta), path(csv) ]
Original CONCOCT GT1000 output

`raw_clustering_csv`

Structure: [ val(meta), path(csv) ]
CSV containing information which subcontig is assigned to which cluster

`pca_original`

Structure: [ val(meta), path(csv) ]
CSV file containing untransformed PCA component values

`pca_transformed`

Structure: [ val(meta), path(csv) ]
CSV file transformed PCA component values

`cluster_table`

Structure: [ val(meta), path(csv) ]
CSV file containing final cluster assignments of original input contigs

`bins`

Structure: [ val(meta), path(fasta) ]
FASTA files containing CONCOCT predicted bin clusters, named numerically
by CONCOCT cluster ID