nf-core/jvarkit/sam2tsv @ 0.0.0-0c7146d
Summary
Convert sam files to tsv files
Get started
Add the following snippet to your workflow script to include this module.
include { JVARKIT_SAM2TSV } from 'nf-core/jvarkit/sam2tsv'
License
MIT License
Process
Name
|
JVARKIT_SAM2TSV |
|---|
Input
2 channels
#1
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test' ] |
|---|---|
bam
file
|
BAM/CRAM file from alignment *.{bam,cram}
|
bai
file
|
BAI/CRAI file from alignment *.{bai,crai}
|
regions_file
file
|
Optional. Restrict to regions listed in a file *.{vcf,bed,gtf,gff,vcf.gz,bed.gz,gtf.gz,gff.gz}
|
#2
tuple
meta2
map
|
Groovy Map containing reference information e.g. [id: 'reference'] |
|---|---|
fasta
file
|
Reference genome *.{fasta,fa}
|
fasta_index
file
|
Reference genome information for fasta index *.{fasta.fai,fa.fai}
|
fasta_dict
file
|
Reference genome information for fasta dict *.{.dict}
|
Output
2 channels
#1
tsv
tuple
meta
map
|
Groovy Map containing TSV information e.g. [ id:'test' ] |
|---|---|
*.tsv
file
|
Output file |
#2
versions
versions.yml
file
|
File containing software versions versions.yml
|
|---|
| Tool | Description | Homepage |
|---|---|---|
| jvarkit | Java utilities for Bioinformatics. | https://github.com/lindenb/jvarkit |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 135d883a43b1a2324b4112cd270cf22e20835533 |
| Release Date | 08 Apr 2026 18:50:23 (UTC) |
| Download URL | https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fsam2tsv/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/jvarkit/sam2tsv/blobs/sha256:e22cc972e60ae633d55b8b061396c19f1e20a43b4e069a64025afa6254ba0399 |
| Size | 2.5 KB |
| Checksum | sha256:e22cc972e60ae633d55b8b061396c19f1e20a43b4e069a64025afa6254ba0399 |
| Downloads | 1 |
| Version | Date | Status | Downloads | Size | Diff |
|---|---|---|---|---|---|
| 0.0.0-0c7146d | 08 Apr 2026 18:50:23 (UTC) | 1 | 2.5 KB | - |