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

meta

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

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

bin

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

versions

File containing software versions

versions.yml