Nextflow Registry | nf-core/artic/aligntrim@0.0.0-0c7146d

nf-core/artic/aligntrim @ 0.0.0-0c7146d

Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @BioWilko

Maintainers: @BioWilko

Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.

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

include { ARTIC_ALIGNTRIM } from 'nf-core/artic/aligntrim'

MIT License

Process

`Name`	`ARTIC_ALIGNTRIM`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`samfile` file	BAM or SAM file containing aligned reads `*.{bam,sam}`
`scheme_bed` file	BED file containing amplicon scheme primer locations `*.bed`
`normalise_depth` integer	Normalise the read depth to this value

`sort_bam` boolean	Optionally sort the BAM file after trimming

Output 4 channels

#1 amp_depth_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.amp_depth_report.tsv` file	TSV report containing mean depth per amplicon `*.amp_depth_report.tsv`

#2 align_trim_report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.align_trim_report.tsv` file	TSV report containing full details of primer trimming for each read / read pair `*.align_trim_report.tsv`

#3 primertrimmed_bam tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`.primertrimmed.bam` file	BAM file with primer sequences soft clipped `.primertrimmed.bam`

#4 versions_align_trim tuple

`${task.process}` string	The name of the process
`align_trim` string	The name of the tool
`align_trim --version \| sed 's/align_trim //'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
align_trim	ARTIC align_trim: A tool for trimming amplicon sequencing primers from aligned reads.	https://github.com/artic-network/align_trim

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:22:49 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fartic%2Faligntrim/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/artic/aligntrim/blobs/sha256:21148aa816d0582b5c26e1fc76ad6e38bcbca185439e7981b2cca91a3a841c23
Size	3.1 KB
Checksum	sha256:21148aa816d0582b5c26e1fc76ad6e38bcbca185439e7981b2cca91a3a841c23
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:22:49 (UTC)		1	3.1 KB	-