Nextflow Registry | nf-core/hifitrimmer/processblast@0.0.0-0c7146d

nf-core/hifitrimmer/processblast @ 0.0.0-0c7146d

Run hifi_trimmer process_blast to process a BLAST search of adapter sequences against PacBio HiFi reads. Primary output is a BED describing regions to exclude, a json of summary information, and an optional hits file.

pacbio bam hifi_trimmer processblast quality control adapter removal

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @sainsachiko

Maintainers: @sainsachiko

Summary

Get started

Add the following snippet to your workflow script to include this module.

include { HIFITRIMMER_PROCESSBLAST } from 'nf-core/hifitrimmer/processblast'

License

MIT License

Process

`Name`	`HIFITRIMMER_PROCESSBLAST`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`blast` file	BLAST TSV output file used by hifi_trimmer (e.g. .blast, .out). Must be generated using "blastn -query -db <adapter_db> -outfmt '6 std qlen'". `*.blast`

#2 tuple

`meta1` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`yaml` file	YAML file contain trimming/filtering configuration for `hifi_trimmer` `*.{yaml,yml}`

Output 4 channels

#1 bed tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.bed.gz` file	Gzipped BED file of selected reads `*.bed.gz`

#2 hits tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.hits` file	Optional hits file produced by hifi_trimmer (may be absent when no hits found or '-hf' is not specified) `*.hits`

#3 summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`*.summary.json` file	JSON summary including trimming and filtering information `*.summary.json`

#4 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 BAM files to output processed FASTA/FASTQ and accompanying summary and hit (optional) files.	https://github.com/sanger-tol/hifi-trimmer

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:47:22 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fhifitrimmer%2Fprocessblast/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/hifitrimmer/processblast/blobs/sha256:b3769cd02326fb17e1f7950a3690fbd7828a83c219280451216395fa96685b3f
Size	3.2 KB
Checksum	sha256:b3769cd02326fb17e1f7950a3690fbd7828a83c219280451216395fa96685b3f
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:47:22 (UTC)		1	3.2 KB	-