Description

Runs the CONCOCT workflow of contig binning

Input

Name (Type)
Description
Pattern

ch_fasta (file)

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

ch_bam (file)

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 (Type)
Description
Pattern

meta (map)

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

coverage_table (file)

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

original_csv (file)

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

raw_clustering_csv (file)

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

pca_original (file)

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

pca_transformed (file)

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

cluster_table (file)

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

bin (file)

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

versions (file)

File containing software versions

versions.yml
included in
mag
included modules and subworkflows
concoct/cutupfasta concoct/concoctcoveragetable concoct/concoct concoct/mergecutupclustering concoct/extractfastabins
maintainer
Github user jfy133
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