nf-core/chopper @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:09:07 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fchopper/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/chopper/blobs/sha256:f0666ea05d038ea7209ab93df0c69adf1a0764cc988ff8f849bee47499304fba |
| Size | 3.1 KB |
| Checksum | sha256:f0666ea05d038ea7209ab93df0c69adf1a0764cc988ff8f849bee47499304fba |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:09:07 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 18:51:41 (UTC) | 3 | 3.1 KB |