mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
48 lines
1.4 KiB
YAML
48 lines
1.4 KiB
YAML
name: samtools_flagstat
|
|
description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type
|
|
keywords:
|
|
- stats
|
|
- mapping
|
|
- 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
|
|
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
|
|
pattern: "*.{bam,cram,sam}"
|
|
- bai:
|
|
type: file
|
|
description: Index for BAM/CRAM/SAM file
|
|
pattern: "*.{bai,crai,sai}"
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- flagstat:
|
|
type: file
|
|
description: File containing samtools flagstat output
|
|
pattern: "*.{flagstat}"
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
authors:
|
|
- "@drpatelh"
|