nf-core/samtools/fixmate @ 0.0.0-0c7146d
Summary
Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs.
Get started
Add the following snippet to your workflow script to include this module.
include { SAMTOOLS_FIXMATE } from 'nf-core/samtools/fixmate'
License
MIT License
Name
|
SAMTOOLS_FIXMATE |
|---|
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] |
|---|---|
input
file
|
BAM/CRAM/SAM file, must be sorted by name, not coordinate *.{bam,cram,sam}
|
bam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{bam}
|
|---|---|
${prefix}.bam
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{bam}
|
sam
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{bam}
|
|---|---|
${prefix}.sam
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{sam}
|
cram
tuple
meta
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{bam}
|
|---|---|
${prefix}.cram
map
|
Groovy Map containing sample information e.g. [ id:'test', single_end:false ] *.{cram}
|
versions_samtools
tuple
${task.process}
string
|
The process the versions were collected from |
|---|---|
samtools
string
|
The tool name |
samtools version | sed '1!d;s/.* //'
string
|
The command used to generate the version of the tool |
| Tool | Description | Homepage |
|---|---|---|
| samtools | SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. These files are generated as output by short read aligners like BWA. | http://www.htslib.org/ |
| Version | 0.0.0-0c7146d |
|---|---|
| Commit ID | 6c4ed3a220310b905a1fc9d04f05be2e0837142b |
| Release Date | 08 Apr 2026 19:33:47 (UTC) |
| Download URL | https://registry.nextflow.io/api/v1/modules/nf-core%2Fsamtools%2Ffixmate/0.0.0-0c7146d/download |
| OCI Store URL | https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/samtools/fixmate/blobs/sha256:de2c00b3f509e44abb560e912da60f409f0b103bc523868693978a283fd9cf53 |
| Size | 3.2 KB |
| Checksum | sha256:de2c00b3f509e44abb560e912da60f409f0b103bc523868693978a283fd9cf53 |
| Downloads | 2 |
| Version | Date | Status | Downloads | Size |
|---|---|---|---|---|
| 0.0.0-6c4ed3a | 23 Apr 2026 15:42:22 (UTC) | 3 | 3.3 KB | |
| 0.0.0-0c7146d | 08 Apr 2026 19:33:47 (UTC) | 2 | 3.2 KB |