mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
e19a9a2474
* new tool: staden_io_lib * update docker containers * add test.yml * add fai index input * typo * fix version.yml * update md5sum * omit md5sum for cram * move scramble to submodule * add missing in/output * remove some comments Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
58 lines
1.6 KiB
YAML
58 lines
1.6 KiB
YAML
name: "stadeniolib_scramble"
|
|
description: Advanced sequence file format conversions
|
|
keywords:
|
|
- sam
|
|
- bam
|
|
- cram
|
|
- compression
|
|
tools:
|
|
- "scramble":
|
|
description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats."
|
|
homepage: "https://github.com/jkbonfield/io_lib"
|
|
documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md"
|
|
tool_dev_url: "https://github.com/jkbonfield/io_lib"
|
|
licence: "['BSD']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: BAM/CRAM/SAM file
|
|
pattern: "*.{bam,cram,sam}"
|
|
- fasta:
|
|
type: file
|
|
description: Reference genome in FASTA format
|
|
pattern: "*.{fa,fasta}"
|
|
- fai:
|
|
type: file
|
|
description: FASTA index file from samtools faidx
|
|
pattern: "*.{fai}"
|
|
- gzi:
|
|
type: file
|
|
description: Optional gzip index file for BAM inputs
|
|
pattern: "*.gzi"
|
|
|
|
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"
|
|
- reads:
|
|
type: file
|
|
description: Converted reads
|
|
pattern: "*.{sam, bam, cram}"
|
|
- gzi:
|
|
type: Optional file
|
|
description: gzip index file for BAM outputs
|
|
pattern: ".{bam.gzi}"
|
|
authors:
|
|
- "@matthdsm"
|