mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
1780cf9bcf
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Add ANGSD doCounts * Prettier * Update main.nf * Apply suggestions from code review * Apply suggestions from code review * Apply suggestions from code review * Try loosening test due to conda * Remove md5 for binary file Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
72 lines
2 KiB
YAML
72 lines
2 KiB
YAML
name: "angsd_docounts"
|
|
description: Calculates base frequency statistics across reference positions from BAM.
|
|
keywords:
|
|
- angsd
|
|
- population genetics
|
|
- allele counts
|
|
- doCounts
|
|
tools:
|
|
- "angsd":
|
|
description: "ANGSD: Analysis of next generation Sequencing Data"
|
|
homepage: "http://www.popgen.dk/angsd/"
|
|
documentation: "http://www.popgen.dk/angsd/"
|
|
tool_dev_url: "https://github.com/ANGSD/angsd"
|
|
doi: "10.1186/s12859-014-0356-4"
|
|
licence: "['GPL v3, MIT']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- bam:
|
|
type: file
|
|
description: A list of BAM or CRAM files
|
|
pattern: "*.{bam,cram}"
|
|
- bai:
|
|
type: file
|
|
description: List of BAM/CRAM index files
|
|
pattern: "*.{bai,csi}"
|
|
- minqfile:
|
|
type: file
|
|
description: File with individual quality score thresholds
|
|
pattern: "*"
|
|
|
|
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"
|
|
- depth_sample:
|
|
type: file
|
|
description: Distribution of sequencing depths
|
|
pattern: "*.depthSample"
|
|
- depth_global:
|
|
type: file
|
|
description: Distribution of sequencing depths
|
|
pattern: "*.depthGlobal"
|
|
- qs:
|
|
type: file
|
|
description: Distribution of scores
|
|
pattern: "*.qs"
|
|
- pos:
|
|
type: file
|
|
description: Various types of depth statistics (depending on value for -dumpCounts)
|
|
pattern: "*.pos.gz"
|
|
- counts:
|
|
type: file
|
|
description: Various types of statistics (related to pos.gz)
|
|
pattern: "*.counts.gz"
|
|
- icounts:
|
|
type: file
|
|
description: Internal format for dumping binary single chrs. Useful for ANGSD contamination
|
|
pattern: "*.icnts.gz"
|
|
|
|
authors:
|
|
- "@jfy133"
|