seqkit_grep
Description¶
Select sequences from a large file based on name/ID
Pipelines¶
This module is used by the following pipelines:
Installation¶
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install seqkit/grep
Tools¶
seqkit¶
Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
sequence |
file | Fasta or fastq file containing sequences to be filtered | *.{fa,fna,faa,fasta,fq,fastq}[.gz] |
pattern |
file | pattern file (one record per line). If no pattern is given, a string can be specified within the args using '-p pattern_string' | *.{txt,tsv} |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
filter |
file | - | |
versions |
file | - |
