From 5c9e50cd53addc807471f90ad2e7e1c03a084888 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Wed, 27 Nov 2024 09:47:39 -0600 Subject: [PATCH 1/5] updated listeria parameter --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 86c15d4..abce9f1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 From 07a1231b5c4b682f774c52baf6394c7d71b1d876 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Wed, 27 Nov 2024 09:50:03 -0600 Subject: [PATCH 2/5] updated changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 90dbd1b..344bc03 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` From 58471c93ec4fd6fa494077c6f4da44cbf7115cd8 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Wed, 27 Nov 2024 09:53:06 -0600 Subject: [PATCH 3/5] updated wordslist --- .wordlist.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.wordlist.txt b/.wordlist.txt index 4eeda68..4fff5c8 100644 --- a/.wordlist.txt +++ b/.wordlist.txt @@ -175,4 +175,4 @@ Christy Marinier Petkau gzipped - +monocytogenes From 42236fdc1ed5f882a0c9bd15e8018808f16f2cc1 Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Wed, 27 Nov 2024 10:15:32 -0600 Subject: [PATCH 4/5] updated changelog --- CHANGELOG.md | 3 ++- nextflow.config | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 344bc03..2956306 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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` @@ -192,6 +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 diff --git a/nextflow.config b/nextflow.config index abce9f1..e4b8e5e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 = '' } From 6e6758b1845ec0674fe51cfbc5524ac681a3dadf Mon Sep 17 00:00:00 2001 From: Matthew Wells Date: Wed, 27 Nov 2024 10:48:38 -0600 Subject: [PATCH 5/5] updated tests for listeria --- tests/pipelines/main.from_assemblies.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/pipelines/main.from_assemblies.nf.test b/tests/pipelines/main.from_assemblies.nf.test index 652f21c..ae8a41c 100644 --- a/tests/pipelines/main.from_assemblies.nf.test +++ b/tests/pipelines/main.from_assemblies.nf.test @@ -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