mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
45 lines
1.3 KiB
YAML
45 lines
1.3 KiB
YAML
|
name: samtools_depth
|
|||
|
|
description: Computes the depth at each position or region.
|
|||
|
|
keywords:
|
|||
|
|
- depth
|
|||
|
|
- samtools
|
|||
|
|
- statistics
|
|||
|
|
- coverage
|
|||
|
|
tools:
|
|||
|
|
- samtools:
|
|||
|
|
description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region
|
|||
|
|
homepage: http://www.htslib.org
|
|||
|
|
documentation: http://www.htslib.org/doc/samtools-depth.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: sorted BAM/CRAM/SAM file
|
|||
|
|
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"
|
|||
|
|
- tsv:
|
|||
|
|
type: file
|
|||
|
|
description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position
|
|||
|
|
pattern: "*.{tsv}"
|
|||
|
|
|
|||
|
|
authors:
|
|||
|
|
- "@louperelo"
|