mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
3f14b1fabe
* add shovill module * removed deprecated shovill module * fix line ending in functions.nf * fix yaml indentation * reduce spades memory usage * update md5sums * remove non reproducible md5sum * Update test.yml Remove last non-reproducible md5sum. * purely cosmetic order change * proper process label, improve output readability Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
59 lines
1.7 KiB
YAML
59 lines
1.7 KiB
YAML
name: shovill
|
|
## TODO nf-core: Add a description of the module and list keywords
|
|
description: Assemble bacterial isolate genomes from Illumina paired-end reads
|
|
keywords:
|
|
- bacterial
|
|
- assembly
|
|
- illumina
|
|
|
|
tools:
|
|
- shovill:
|
|
## TODO nf-core: Add a description and other details for the software below
|
|
description: Microbial assembly pipeline for Illumina paired-end reads
|
|
homepage: https://github.com/tseemann/shovill
|
|
documentation: https://github.com/tseemann/shovill/blob/master/README.md
|
|
licence: ['GPL v2']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- reads:
|
|
type: file
|
|
description: List of input paired-end FastQ files
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- version:
|
|
type: file
|
|
description: File containing software version
|
|
pattern: "*.{version.txt}"
|
|
- contigs:
|
|
type: file
|
|
description: The final assembly produced by Shovill
|
|
pattern: "contigs.fa"
|
|
- corrections:
|
|
type: file
|
|
description: List of post-assembly corrections made by Shovill
|
|
pattern: "shovill.corrections"
|
|
- log:
|
|
type: file
|
|
description: Full log file for bug reporting
|
|
pattern: "shovill.log"
|
|
- raw_contigs:
|
|
type: file
|
|
description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet)
|
|
pattern: "{skesa,spades,megahit,velvet}.fasta"
|
|
- gfa:
|
|
type: file
|
|
description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet
|
|
pattern: "contigs.{fastg,gfa,LastGraph}"
|
|
|
|
authors:
|
|
- "@rpetit3"
|