nf-core/chopper @ 0.0.0-0c7146d
Summary
Filter and trim long read data.
Get started
Add the following snippet to your workflow script to include this module.
include { CHOPPER } from 'nf-core/chopper'
License
MIT License
Process
Name
|
CHOPPER |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
fastq
file
|
FastQ with reads from long read sequencing e.g. PacBio or ONT *.{fastq.gz}
|
fasta
file
|
An optional reference fasta file against which to remove reads that align to it. *.fasta
|
|---|
Output
2 channels
#1
fastq
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.fastq.gz
file
|
Filtered and trimmed FastQ file *.{fastq.gz}
|
#2
versions_chopper
tuple
${task.process}
string
|
The name of the process |
|---|---|
chopper
string
|
The name of the tool |
chopper --version 2>&1 | cut -d ' ' -f 2
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| zcat | zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output. | n/a |
| chopper | A rust command line for filtering and trimming long reads. | https://github.com/wdecoster/chopper |
| gzip | Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77). | n/a |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:30:38 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fchopper/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/chopper/blobs/sha256:598e41aa8154bb6abbb2831feaec49def9b7a25a0f91f2bb60240ff5f5a95796 |
| Size | 3.2 KB |
| Checksum | sha256:598e41aa8154bb6abbb2831feaec49def9b7a25a0f91f2bb60240ff5f5a95796 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:30:38 (UTC) | 1 | 3.2 KB | - |