nf-core/jvarkit/sam2tsv @ 0.0.0-6c4ed3a
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 | 0.0.0-6c4ed3a |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 23 Apr 2026 15:26:25 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fjvarkit%2Fsam2tsv/0.0.0-6c4ed3a/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/jvarkit/sam2tsv/blobs/sha256:5d8ce42da78667666d883a4c536e337de34e00d25c31c326745893f2aa61129c |
| Size | 2.5 KB |
| Checksum | sha256:5d8ce42da78667666d883a4c536e337de34e00d25c31c326745893f2aa61129c |
| Downloads | 3 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:26:25 (UTC) | 3 | 2.5 KB | |
| 0.0.0-3fc6d40 | 22 Apr 2026 15:18:24 (UTC) | 4 | 2.5 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:12:14 (UTC) | 3 | 2.5 KB |