fetchtool_assembly
Description¶
Microbiome Informatics ENA fetch tool
Installation¶
ebi-metagenomics/fetchtool/assembly
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install fetchtool/assembly
Tools¶
fetchtool¶
Utility to fetch public and private RAW read and assembly files from the ENA
- github.com/EBI-Metagenomics/fetch_tool/
- github.com/EBI-Metagenomics/fetch_tool/
- A, p, a, c, h, e, , L, i, c, e, n, s, e, , 2, ., 0
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
- |
assembly_accession |
string | The assembly ENA accession | - |
fetchtool_config |
file | Configuration file, https://github.com/EBI-Metagenomics/fetch_tool/#configuration-file | *.json |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
assembly |
file | The assembly contigs fasta file, gzipped | *.fasta.gz |
versions |
file | File containing software versions | versions.yml |
