mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 13:43:09 +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>
57 lines
1.5 KiB
YAML
57 lines
1.5 KiB
YAML
name: damageprofiler
|
|
description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
|
|
keywords:
|
|
- damage
|
|
- deamination
|
|
- miscoding lesions
|
|
- C to T
|
|
- ancient DNA
|
|
- aDNA
|
|
- palaeogenomics
|
|
- archaeogenomics
|
|
- palaeogenetics
|
|
- archaeogenetics
|
|
tools:
|
|
- damageprofiler:
|
|
description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage
|
|
homepage: https://github.com/Integrative-Transcriptomics/DamageProfiler
|
|
documentation: https://damageprofiler.readthedocs.io/
|
|
tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler
|
|
doi: "10.1093/bioinformatics/btab190"
|
|
licence: ["GPL v3"]
|
|
|
|
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}"
|
|
- fasta:
|
|
type: file
|
|
description: OPTIONAL FASTA reference file
|
|
pattern: "*.{fasta,fna,fa}"
|
|
- fai:
|
|
type: file
|
|
description: OPTIONAL FASTA index file from samtools faidx
|
|
pattern: "*.{fai}"
|
|
- specieslist:
|
|
type: file
|
|
description: OPTIONAL text file with list of target reference headers
|
|
pattern: "*.{txt}"
|
|
|
|
output:
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- results:
|
|
type: dir
|
|
description: DamageProfiler results directory
|
|
pattern: "*/*"
|
|
|
|
authors:
|
|
- "@jfy133"
|