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updated listeria parameter #142

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merged 5 commits into from
Nov 27, 2024
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Merged

updated listeria parameter #142

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5c9e50c
updated listeria parameter
mattheww95 Nov 27, 2024
07a1231
updated changelog
mattheww95 Nov 27, 2024
58471c9
updated wordslist
mattheww95 Nov 27, 2024
42236fd
updated changelog
mattheww95 Nov 27, 2024
6e6758b
updated tests for listeria
mattheww95 Nov 27, 2024
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2 changes: 1 addition & 1 deletion .wordlist.txt
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Expand Up @@ -175,4 +175,4 @@ Christy
Marinier
Petkau
gzipped

monocytogenes
4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -3,7 +3,7 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## Unreleased
## [0.5.0] - 2024-11-27

### `Added`

Expand All @@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- RASUSA now used for down sampling of Nanopore or PacBio data. [PR 125](https://github.com/phac-nml/mikrokondo/pull/125)

- Default *Listeria* quality control parameters apply only to *monocytogenes* now. [PR 142](https://github.com/phac-nml/mikrokondo/pull/142)

### `Updated`

Expand Down Expand Up @@ -191,6 +192,7 @@ Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trim

- Added integration testing using [nf-test](https://www.nf-test.com/).

[0.5.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.5.0
[0.4.2]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.2
[0.4.1]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.1
[0.4.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.0
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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -790,7 +790,7 @@ params {
min_average_coverage = 40
}
listeria {
search = "Listeria"
search = "Listeria monocytogenes"
raw_average_quality = 30
min_n50 = 50000
max_n50 = 3200000
Expand Down Expand Up @@ -1206,7 +1206,7 @@ manifest {
description = """Mikrokondo"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '0.4.2'
version = '0.5.0'
defaultBranch = 'main'
doi = ''
}
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2 changes: 1 addition & 1 deletion tests/pipelines/main.from_assemblies.nf.test
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Expand Up @@ -555,7 +555,7 @@ nextflow_pipeline {
assert listeria_metadata."Length Value" == 2944528
assert listeria_metadata."nr contigs Status" == "PASSED"
assert listeria_metadata."nr contigs Value" == 1
assert listeria_metadata."QC Summary" == "FAILED Species ID: Listeria monocytogenes; Passed Tests: 3/4; Organism QC Criteria: Listeria"
assert listeria_metadata."QC Summary" == "FAILED Species ID: Listeria monocytogenes; Passed Tests: 3/4; Organism QC Criteria: Listeria monocytogenes"

assert listeria_metadata."Downsampled" == false

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