mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
08b71fa85f
* 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 * Add GUNC download_db and run commands * Bump with version without zgrep * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * Harshil formatting * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: gunc_run
|
|
description: Detection of Chimerism and Contamination in Prokaryotic Genomes
|
|
keywords:
|
|
- prokaryote
|
|
- assembly
|
|
- genome
|
|
- quality control
|
|
- chimeras
|
|
tools:
|
|
- gunc:
|
|
description: Python package for detection of chimerism and contamination in prokaryotic genomes.
|
|
homepage: https://grp-bork.embl-community.io/gunc/
|
|
documentation: https://grp-bork.embl-community.io/gunc/
|
|
tool_dev_url: https://github.com/grp-bork/gunc
|
|
doi: "10.1186/s13059-021-02393-0"
|
|
licence: ['GNU General Public v3 or later (GPL v3+)']
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- fasta:
|
|
type: file
|
|
description: FASTA file containing contig (bins)
|
|
pattern: "*.fa"
|
|
- db:
|
|
type: file
|
|
description: GUNC database file
|
|
pattern: "*.dmnd"
|
|
|
|
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"
|
|
- maxcss_levels_tsv:
|
|
type: file
|
|
description: Output file with scores for a taxonomic level with the highest CSS score
|
|
pattern: "*.tsv"
|
|
- all_levels_tsv:
|
|
type: file
|
|
description: Optional output file with results for each taxonomic level
|
|
pattern: "*.tsv"
|
|
|
|
authors:
|
|
- "@jfy133"
|