Generate the input coverage table for CONCOCT using a BEDFile
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bed{:bash}
:file
BED file describing where each contig was cut up (typically output from CONCOCT’s cut_up_fasta.py)
*.bed
bamfiles{:bash}
A single or list of BAM files of reads mapped back to original contigs (prior cutting up)
*.bam
baifiles{:bash}
A single or list of BAM index files (.bai) corresponding to BAM
tsv{:bash}
*.tsv{:bash}
Contig coverage table
*.tsv
versions_concoct{:bash}
${task.process}{:bash}
:string
The name of the process
concoct{:bash}
The name of the tool
concoct --version | cut -d " " -f2{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
Clustering cONtigs with COverage and ComposiTion
