combined_gene_caller
Description¶
MGnify combined gene calling. This workflow runs gene prediction with Pyrodigal and FragGeneScanRS, and then combines the resulting predictions. The merged output contains all the gene predictions from Pyrodigal, along with genes predicted by FragGeneScanRS that do not overlap with any Pyrodigal gene. Optionally, it can mask (remove) genes that overlap with regions from a masking file.
Installation¶
ebi-metagenomics/combined_gene_caller
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install combined_gene_caller
Keywords: gene finding, gene prediction, prokaryotes, microbial
Components¶
This subworkflow uses the following components:
pyrodigal(module)fraggenescanrs(module)combinedgenecaller/merge(module)
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
ch_assembly |
map | An input channel containing the following files: - assembly: One or more assembly or genome contigs fasta file. Structure: [ meta, assembly ] | - |
ch_mask_file |
map | An input channel containing the following files: - mask: One or more tblout files generated by Infernal cmscan or cmsearch. Structure: [ meta, mask_file ] | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
faa |
file | protein translations of the predicted genes | *.faa |
ffn |
file | nucleotide sequences of the predicted genes | *.ffn |
gff |
file | gene annotations in gff format | *.gff |
versions |
file | File containing software versions | versions.yml |