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 | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:37:20 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fentrezdirect%2Fxtract/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/entrezdirect/xtract/blobs/sha256:7f91e5215155751e5187e5bf833e3443f47ab41909d63386bd32ae9f8221bd7b |
| Size | 2.8 KB |
| Checksum | sha256:7f91e5215155751e5187e5bf833e3443f47ab41909d63386bd32ae9f8221bd7b |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:37:20 (UTC) | 1 | 2.8 KB | - |