nf-core/sratools/fasterqdump @ 0.0.0-6c4ed3a
Summary
Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA).
Get started
Add the following snippet to your workflow script to include this module.
include { SRATOOLS_FASTERQDUMP } from 'nf-core/sratools/fasterqdump'
License
MIT License
Process
Name
|
SRATOOLS_FASTERQDUMP |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
sra
directory
|
Directory containing ETL data for the given SRA. */*.sra
|
ncbi_settings
file
|
An NCBI user settings file. *.mkfg
|
|---|
certificate
file
|
Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit *.cart
|
|---|
Output
3 channels
#1
reads
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fastq.gz
file
|
Extracted FASTQ file or files if the sequencing reads are paired-end. *.fastq.gz
|
#2
versions_pigz
tuple
${task.process}
string
|
The name of the process |
|---|---|
pigz
string
|
The name of the tool |
pigz --version 2>&1 | sed 's/pigz //g'
eval
|
The expression to obtain the version of the tool |
#3
versions_sratools
tuple
${task.process}
string
|
The name of the process |
|---|---|
sratools
string
|
The name of the tool |
prefetch --version 2>&1 | grep -Eo '[0-9.]+'
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| sratools | SRA Toolkit and SDK from NCBI | https://github.com/ncbi/sra-tools |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:47:11 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsratools%2Ffasterqdump/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/sratools/fasterqdump/blobs/sha256:673aa532bc4768299ae841facc6901edfb02fbfcbe1e0e71404b1c1d7cd4446e |
| Size | 3.2 KB |
| Checksum | sha256:673aa532bc4768299ae841facc6901edfb02fbfcbe1e0e71404b1c1d7cd4446e |
| Downloads | 4 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:47:11 (UTC) | 4 | 3.2 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:40:18 (UTC) | 3 | 3.2 KB |