nf-core/seqkit/grep @ 0.0.0-3fc6d40
Summary
Select sequences from a large file based on name/ID
Get started
Add the following snippet to your workflow script to include this module.
include { SEQKIT_GREP } from 'nf-core/seqkit/grep'
License
MIT License
Process
Name
|
SEQKIT_GREP |
|---|
Input
2 channels
#1
tuple
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
2 channels
#1
filter
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.{fa,fq,fa.gz,fq.gz}
file
|
Fasta or fastq file containing the filtered sequences. Will be gzipped if the input file was gzipped. |
#2
versions_seqkit
tuple
${task.process}
string
|
The name of the process |
|---|---|
seqkit
string
|
The name of the tool |
seqkit version | sed "s/seqkit v//"
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| seqkit | Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. | https://bioinf.shenwei.me/seqkit/usage/ |
| Version | 0.0.0-3fc6d40 |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 22 Apr 2026 15:30:21 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fseqkit%2Fgrep/0.0.0-3fc6d40/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/seqkit/grep/blobs/sha256:e63e775d5f0084facfb8c5dbda51777cd93ccf9e8cf1b75430736a4e51a0dd08 |
| Size | 2.8 KB |
| Checksum | sha256:e63e775d5f0084facfb8c5dbda51777cd93ccf9e8cf1b75430736a4e51a0dd08 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:44:26 (UTC) | 3 | 2.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:30:21 (UTC) | 3 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:36:34 (UTC) | 3 | 2.8 KB |