mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
81d65d4978
* Samtools fixmate module * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/fixmate/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf * Update modules/samtools/fixmate/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update meta.yml Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
49 lines
1.6 KiB
YAML
49 lines
1.6 KiB
YAML
name: samtools_fixmate
|
|
description: 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.
|
|
keywords:
|
|
- fixmate
|
|
- samtools
|
|
- insert size
|
|
- repair
|
|
- bam
|
|
- paired
|
|
- read pairs
|
|
tools:
|
|
- samtools:
|
|
description: |
|
|
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.
|
|
homepage: http://www.htslib.org/
|
|
documentation: http://www.htslib.org/doc/samtools.html
|
|
tool_dev_url: https://github.com/samtools/samtools
|
|
doi: 10.1093/bioinformatics/btp352
|
|
licence: ['MIT']
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: BAM/CRAM/SAM file, must be sorted by name, not coordinate
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- bam:
|
|
type: file
|
|
description: A BAM/CRAM/SAM file with mate information added and/or proper pairs recalled
|
|
pattern: "*.{bam,cram,sam}"
|
|
|
|
authors:
|
|
- "@sppearce"
|