nf-core/hifitrimmer/filterbam @ 0.0.0-0c7146d
Summary
Run hifi_trimmer filter_bam to filter and trim adapter hits from PacBio HiFi reads (BAM/FASTA/FASTQ) using BLAST against adapter sequences. Primary output is filtered FASTA/FASTQ.
Get started
Add the following snippet to your workflow script to include this module.
include { HIFITRIMMER_FILTERBAM } from 'nf-core/hifitrimmer/filterbam'
License
MIT License
Process
Name
|
HIFITRIMMER_FILTERBAM |
|---|
Input
1 channel
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
input
file
|
Input BAM/FASTA/FASTQ file to filter *.{bam,fa,fasta,fa.gz,fasta.gz,fastq,fq,fastq.gz,fq.gz}
|
bed
file
|
Input gzipped bed file contains regions to filter/trim *.bed.gz
|
Output
3 channels
#1
filtered
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.fast{q,a}.gz
file
|
Gzipped FASTA/FASTQ produced by hifi_trimmer *.fast{q,a}.gz
|
#2
versions_samtools
tuple
${task.process}
string
|
Name of the process |
|---|---|
samtools
string
|
Name of the tool |
samtools --version | head -1 | sed -e "s/samtools //"
eval
|
The expression to obtain the version of the tool |
#3
versions_hifitrimmer
tuple
${task.process}
string
|
The name of the process |
|---|---|
hifi_trimmer
string
|
The name of the tool |
hifi_trimmer --version | cut -d' ' -f3
eval
|
The expression to obtain the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| hifi_trimmer | hifi_trimmer: tools for processing HiFi read BLAST results and filtering/trimming read files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files. | https://github.com/sanger-tol/hifi-trimmer |
| samtools | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. | http://www.htslib.org/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:47:19 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhifitrimmer%2Ffilterbam/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hifitrimmer/filterbam/blobs/sha256:16cd806a5ea06316f18369cf9da99d94c64af347cf28067a7ecd156a78407d61 |
| Size | 3.3 KB |
| Checksum | sha256:16cd806a5ea06316f18369cf9da99d94c64af347cf28067a7ecd156a78407d61 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:47:19 (UTC) | 1 | 3.3 KB | - |