nf-core/bioawk @ 0.0.0-e2d3f0d
Summary
Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats.
Get started
Add the following snippet to your workflow script to include this module.
include { BIOAWK } from 'nf-core/bioawk'
License
MIT License
Name
|
BIOAWK |
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meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
Input biological sequence file (optionally gzipped) to be manipulated via the program specified in *.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}
|
program_file
file
|
Optional file containing logic for awk to execute. If you don't wish to use a file, you can use *
|
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disable_redirect_output
boolean
|
Disable the redirection of awk output to a given file. This is useful if you want to use awk's built-in redirect to write files instead of the shell's redirect. |
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output_file_extension
string
|
The suffix to add to the output file name. |
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output
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
*.${output_file_extension}
file
|
Manipulated version of the input sequence file. |
versions_bioawk
tuple
${task.process}
string
|
The name of the process |
|---|---|
bioawk
string
|
The name of the tool |
1.0
string
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| bioawk | BWK awk modified for biological data | https://github.com/lh3/bioawk |
| Version | 0.0.0-e2d3f0d |
|---|---|
| Commit ID | e2d3f0ddf4a74a4a9031f3caea2e9deaec5a440b |
| Release Date | 28 Apr 2026 21:15:05 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fbioawk/0.0.0-e2d3f0d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/bioawk/blobs/sha256:a45b6101aafeabbd0d6a4e53149ec130f124d81a7ecc3cb269b9fe62472b0ee4 |
| Size | 3.2 KB |
| Checksum | sha256:a45b6101aafeabbd0d6a4e53149ec130f124d81a7ecc3cb269b9fe62472b0ee4 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-e2d3f0d | 28 Apr 2026 21:15:05 (UTC) | 1 | 3.2 KB | ↔ | |
| 0.0.0-0c7146d | 08 Apr 2026 18:26:47 (UTC) | 1 | 3.2 KB | - |