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nf-core/cobrameta @ 0.0.0-6c4ed3a

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

cobra contig scaffold assembly extension virus phage
Latest version: 0.0.0-6c4ed3a
Total downloads: 10
Source: nf-core/modules
Authors: @CarsonJM
Maintainers: @CarsonJM

Summary

A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly.

Get started

Add the following snippet to your workflow script to include this module.

include { COBRAMETA } from 'nf-core/cobrameta'

License

MIT License

Process
Name COBRAMETA
Input 7 channels
#1 tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1' ]
fasta file

Assembly file (contigs/scaffolds) in FASTA format

 *.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}
#2 tuple
meta2 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
coverage file

TSV file with 2 columns containing 1) the contig/scaffold id and 2) the coverage depth of the sequence specified in column 1

 *.{tsv,txt}
#3 tuple
meta3 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
query file

File containing the query contigs that the user wants COBRA to extend. This can be provided in one-column TXT or FASTA format. (The IDs must match the IDs in the --fasta file exactly)

 *.{txt,fasta}
#4 tuple
meta4 map

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
bam file

Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly to the resulting assembly FASTA

 *.{bam,cram,sam}
assembler string

The name of the tool used to assemble contigs

 {metaspades,megahit,idba}
mink integer

The minimum kmer size used to assemble contigs

 [0-9]+
maxk integer

The maximum kmer size used to assemble contigs

 [0-9]+
Output 9 channels
#1 log tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}/log file

Log file containing the contents of each processing

 ${prefix}/log
#2 orphan_end tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}/COBRA_category_iii_orphan_end.fasta.gz file

Gzipped FASTA file containing query contigs that do not shared the "expected overlap length" with other contigs

 ${prefix}/COBRA_category_iii_orphan_end.fasta.gz
#3 self_circular tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}/COBRA_category_i_self_circular.fasta.gz file

fasta file

 */COBRA_category_i_self_circular.fasta.gz
#4 versions_cobra tuple
${task.process} string

The name of the process
cobra string

The name of the tool
cobra-meta --version 2>&1 | sed 's/^.*cobra v//' eval

The expression to obtain the version of the tool
#5 extended_failed tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz file

Gzipped FASTA file containing query contigs that could not be extended due to COBRA rules

 ${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz
#6 joining_summary tuple
meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
${prefix}/COBRA_joining_summary.txt