nf-core/gem3/gem3mapper @ 0.0.0-0c7146d
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 | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:43:49 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fgem3%2Fgem3mapper/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/gem3/gem3mapper/blobs/sha256:2751ee09ac6b1b0cb797b58ee92f1a0e68416db5d4b4be88c2b514216e4dd97a |
| Size | 2.5 KB |
| Checksum | sha256:2751ee09ac6b1b0cb797b58ee92f1a0e68416db5d4b4be88c2b514216e4dd97a |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:43:49 (UTC) | 1 | 2.5 KB | - |