mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +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>
52 lines
1.4 KiB
YAML
52 lines
1.4 KiB
YAML
name: bbmap_bbduk
|
|
description: Adapter and quality trimming of sequencing reads
|
|
keywords:
|
|
- trimming
|
|
- adapter trimming
|
|
- quality trimming
|
|
tools:
|
|
- bbmap:
|
|
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
|
|
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
|
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
|
|
tool_dev_url: None
|
|
doi: ""
|
|
licence: ["UC-LBL license (see package)"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: |
|
|
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
|
|
respectively.
|
|
- contaminants:
|
|
type: file
|
|
description: |
|
|
Reference files containing adapter and/or contaminant sequences for sequence kmer matching
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: The trimmed/modified fastq reads
|
|
pattern: "*fastq.gz"
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- log:
|
|
type: file
|
|
description: Bbduk log file
|
|
pattern: "*bbduk.log"
|
|
|
|
authors:
|
|
- "@MGordon09"
|