nf-core/entrezdirect/xtract @ 0.0.0-0c7146d
Summary
Queries an NCBI database using an UID
Get started
Add the following snippet to your workflow script to include this module.
include { ENTREZDIRECT_XTRACT } from 'nf-core/entrezdirect/xtract'
License
MIT License
Process
Name
|
ENTREZDIRECT_XTRACT |
|---|
Input
4 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
xml_input
file
|
XML text file containing query results from database. |
pattern
string
|
String in xml_input that encloses element to search. |
|---|
element
string
|
Space-delimited strings that will be converted to columns. |
|---|
sep
string
|
Separator/delimiter between columns (for instance "," or "\t"). |
|---|
Output
2 channels
#1
txt
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.txt
file
|
Text file *.txt
|
#2
versions_xtract
tuple
${task.process}
string
|
The name of the process |
|---|---|
xtract
string
|
The name of the tool |
xtract -version 2>&1
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| entrezdirect | Entrez Direct (EDirect) is a method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. Functions take search terms from command line arguments. Individual operations are combined to build multi-step queries. Record retrieval and formatting normally complete the process. | https://www.ncbi.nlm.nih.gov/books/NBK179288/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 18:58:49 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fentrezdirect%2Fxtract/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/entrezdirect/xtract/blobs/sha256:8557a5df968667dec2e9632ab241f7ba07a5f2b2569b582b8d0e75508752326a |
| Size | 2.7 KB |
| Checksum | sha256:8557a5df968667dec2e9632ab241f7ba07a5f2b2569b582b8d0e75508752326a |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:15:02 (UTC) | 1 | 2.8 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:10:57 (UTC) | 1 | 2.8 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:58:49 (UTC) | 1 | 2.7 KB |