nf-core/artic/aligntrim @ 0.0.0-c24122a
Summary
Standalone version of fieldbioinformatics aligntrim. Soft clips amplicon scheme primer sites in BAM/SAM files.
Get started
Add the following snippet to your workflow script to include this module.
include { ARTIC_ALIGNTRIM } from 'nf-core/artic/aligntrim'
License
MIT License
Name
|
ARTIC_ALIGNTRIM |
|---|
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
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 |
|---|
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
|
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
|
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
|
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-c24122a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 11 Apr 2026 15:00:05 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fartic%2Faligntrim/0.0.0-c24122a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/artic/aligntrim/blobs/sha256:6d45edd255ab4171bd976720183b42efdc5a38c96a336791eb227be85b5906b6 |
| Size | 3.1 KB |
| Checksum | sha256:6d45edd255ab4171bd976720183b42efdc5a38c96a336791eb227be85b5906b6 |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:02:47 (UTC) | 3 | 3.1 KB | |
| 0.0.0-c24122a | 11 Apr 2026 15:00:05 (UTC) | 3 | 3.1 KB | |
| 0.0.0-56a9b6d | 10 Apr 2026 15:00:26 (UTC) | 3 | 3.1 KB | |
| 0.0.0-0c7146d | 08 |