mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
bd0fa881f6
* changing mv by gzip * changing mv by gzip * first module creation * add test.yml * add flye to pyestes_modules.yml * update flye module * delete functions.nf * generate test.yml * fix contains from test.yml * test file assembly_info.txt with regex * check that file contains at least contig_1 * fix typo in contains * update version * split fastq file for raw runs * use asm-coverage to reduce memory usage * fix module name error * add genome-size * decrease coverage * change test data for raw runs * add coverage and genome size * Apply comments from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * after many trys, add a stub run * remove md5sum for stub run * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix review comments * Apply suggestions from code review Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> * no hardcoded version in stub run * Update modules/flye/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: SusiJo <43847534+SusiJo@users.noreply.github.com> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
69 lines
1.9 KiB
YAML
69 lines
1.9 KiB
YAML
name: "flye"
|
|
description: De novo assembler for single molecule sequencing reads
|
|
keywords:
|
|
- assembly
|
|
- genome
|
|
- de novo
|
|
- genome assembler
|
|
- single molecule
|
|
tools:
|
|
- "flye":
|
|
description: "Fast and accurate de novo assembler for single molecule sequencing reads"
|
|
homepage: "https://github.com/fenderglass/Flye"
|
|
documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md"
|
|
tool_dev_url: "https://github.com/fenderglass/Flye"
|
|
doi: "10.1038/s41592-020-00971-x"
|
|
licence: "['BSD-3-clause']"
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test' ]
|
|
- reads:
|
|
type: file
|
|
description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format.
|
|
pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}"
|
|
- mode:
|
|
type: value
|
|
description: Flye mode depending on the input data (source and error rate)
|
|
pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test' ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- fasta:
|
|
type: file
|
|
description: Assembled FASTA file
|
|
pattern: "*.fasta.gz"
|
|
- gfa:
|
|
type: file
|
|
description: Repeat graph in gfa format
|
|
pattern: "*.gfa.gz"
|
|
- gv:
|
|
type: file
|
|
description: Repeat graph in gv format
|
|
pattern: "*.gv.gz"
|
|
- txt:
|
|
type: file
|
|
description: Extra information and statistics about resulting contigs
|
|
pattern: "*.txt"
|
|
- log:
|
|
type: file
|
|
description: Flye log file
|
|
pattern: "*.log"
|
|
- json:
|
|
type: file
|
|
description: Flye parameters
|
|
pattern: "*.json"
|
|
|
|
authors:
|
|
- "@mirpedrol"
|