nf-core/gem3/gem3mapper @ 0.0.0-6c4ed3a
Summary
Performs fastq alignment to a fasta reference using using gem3-mapper
Get started
Add the following snippet to your workflow script to include this module.
include { GEM3_GEM3MAPPER } from 'nf-core/gem3/gem3mapper'
License
MIT License
Process
Name
|
GEM3_GEM3MAPPER |
|---|
Input
3 channels
#1
tuple
meta
map
|
Groovy Map containing reference/index information e.g. [ id:'test' ] |
|---|---|
gem
file
|
GEM3 genome index files *.{gem}
|
#2
tuple
meta2
map
|
Groovy Map containing sample information e.g. |
|---|---|
fastq
file
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. *.{fastq,fq,fastq.gz,fq.gz}
|
sort_bam
boolean
|
use samtools sort (true) or samtools view (false) true or false
|
|---|
Output
2 channels
#1
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. |
|---|---|
*.bam
file
|
Sorted BAM/CRAM/SAM file *.{bam,cram,sam}
|
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| gem3 | The GEM indexer (v3). | https://github.com/smarco/gem3-mapper |
| Version | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:20:58 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fgem3%2Fgem3mapper/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/gem3/gem3mapper/blobs/sha256:276443772383cc46635f7b9a3099e8d6c9187c0ceffb8c7a1dca8784bca8a32a |
| Size | 2.5 KB |
| Checksum | sha256:276443772383cc46635f7b9a3099e8d6c9187c0ceffb8c7a1dca8784bca8a32a |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:20:58 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:13:43 (UTC) | 3 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:05:26 (UTC) | 3 | 2.5 KB |