mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-24 14:19:55 +00:00
54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
|
name: samtools_stats
|
||
|
|
description: Produces comprehensive statistics from SAM/BAM/CRAM file
|
||
|
|
keywords:
|
||
|
|
- statistics
|
||
|
|
- counts
|
||
|
|
- bam
|
||
|
|
- sam
|
||
|
|
- cram
|
||
|
|
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: hhttp://www.htslib.org/doc/samtools.html
|
||
|
|
doi: 10.1093/bioinformatics/btp352
|
||
|
|
licence: ["MIT"]
|
||
|
|
input:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- input:
|
||
|
|
type: file
|
||
|
|
description: BAM/CRAM file from alignment
|
||
|
|
pattern: "*.{bam,cram}"
|
||
|
|
- input_index:
|
||
|
|
type: file
|
||
|
|
description: BAI/CRAI file from alignment
|
||
|
|
pattern: "*.{bai,crai}"
|
||
|
|
- fasta:
|
||
|
|
type: optional file
|
||
|
|
description: Reference file the CRAM was created with
|
||
|
|
pattern: "*.{fasta,fa}"
|
||
|
|
output:
|
||
|
|
- meta:
|
||
|
|
type: map
|
||
|
|
description: |
|
||
|
|
Groovy Map containing sample information
|
||
|
|
e.g. [ id:'test', single_end:false ]
|
||
|
|
- stats:
|
||
|
|
type: file
|
||
|
|
description: File containing samtools stats output
|
||
|
|
pattern: "*.{stats}"
|
||
|
|
- versions:
|
||
|
|
type: file
|
||
|
|
description: File containing software versions
|
||
|
|
pattern: "versions.yml"
|
||
|
|
authors:
|
||
|
|
- "@drpatelh"
|
||
|
|
- "@FriederikeHanssen"
|