mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
359f721cc9
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>
62 lines
2 KiB
YAML
62 lines
2 KiB
YAML
name: megahit
|
|
description: An ultra-fast metagenomic assembler for large and complex metagenomics
|
|
keywords:
|
|
- megahit
|
|
- denovo
|
|
- assembly
|
|
- debruijn
|
|
- metagenomics
|
|
tools:
|
|
- megahit:
|
|
description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"
|
|
homepage: https://github.com/voutcn/megahit
|
|
documentation: https://github.com/voutcn/megahit
|
|
tool_dev_url: https://github.com/voutcn/megahit
|
|
doi: "10.1093/bioinformatics/btv033"
|
|
licence: ['GPL v3']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed)
|
|
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 in gzipped or uncompressed FASTQ or FASTA format.
|
|
|
|
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"
|
|
- contigs:
|
|
type: file
|
|
description: Final final contigs result of the assembly in FASTA format.
|
|
pattern: "*.contigs.fa.gz"
|
|
- k_contigs:
|
|
type: file
|
|
description: Contigs assembled from the de Bruijn graph of order-K
|
|
pattern: "k*.contigs.fa.gz"
|
|
- addi_contigs:
|
|
type: file
|
|
description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K
|
|
pattern: "k*.addi.fa.gz"
|
|
- local_contigs:
|
|
type: file
|
|
description: Contigs of the locally assembled contigs for k=K
|
|
pattern: "k*.local.fa.gz"
|
|
- kfinal_contigs:
|
|
type: file
|
|
description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty
|
|
pattern: "k*.final.contigs.fa.gz"
|
|
|
|
authors:
|
|
- "@jfy133"
|