nf-core_modules/modules/gunc/run/meta.yml
James A. Fellows Yates 08b71fa85f
New module: gunc run (+ gunc downloaddb) (#880)
* 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>
2021-11-03 17:01:23 +01:00

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"