mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.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"
|