diff --git a/CHANGELOG.md b/CHANGELOG.md index 8fa13bc2..ef651d28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,13 @@ 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). -## [[1.2.1](https://github.com/sanger-tol/genomenote/releases/tag/1.2.1)] [2024-07-12] +## [[1.2.2](https://github.com/sanger-tol/genomenote/releases/tag/1.2.2)] - Pyrenean Mountain Dog (patch 2) - [2024-09-10] + +### Enhancements & fixes + +- Bugfix: don't run Busco in scratch mode for large genomes as it takes too much space on /tmp + +## [[1.2.1](https://github.com/sanger-tol/genomenote/releases/tag/1.2.1)] - Pyrenean Mountain Dog (patch 1) - [2024-07-12] ### Enhancements & fixes @@ -40,13 +46,13 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i | ------------- | ------------- | | | --cool_order | -## [[1.1.2](https://github.com/sanger-tol/genomenote/releases/tag/1.1.2)] [2024-04-29] +## [[1.1.2](https://github.com/sanger-tol/genomenote/releases/tag/1.1.2)] - Golden Retriever (patch 2) - [2024-04-29] ### Enhancements & fixes - Bugfix: the BAM still needs to be filtered with `-F0x400` -## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] [2024-02-26] +## [[1.1.1](https://github.com/sanger-tol/genomenote/releases/tag/1.1.1)] - Golden Retriever (patch 1) - [2024-02-26] ### Enhancements & fixes diff --git a/CITATION.cff b/CITATION.cff index 8a350dff..44c3f427 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,16 +2,16 @@ # Visit https://bit.ly/cffinit to generate yours today! cff-version: 1.2.0 -title: sanger-tol/genomenote v1.2.1 +title: sanger-tol/genomenote v1.2.2 message: >- If you use this software, please cite it using the metadata from this file. type: software authors: - - given-names: Cibin - family-names: Sadasivan Baby + - given-names: Tyler + family-names: Chafin affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0002-8538-276X" + orcid: "https://orcid.org/0000-0001-8687-5905" - given-names: Matthieu family-names: Muffato affiliation: Wellcome Sanger Institute @@ -20,12 +20,16 @@ authors: family-names: Qi affiliation: Wellcome Sanger Institute orcid: "https://orcid.org/0000-0003-1262-8973" + - given-names: Cibin + family-names: Sadasivan Baby + affiliation: Wellcome Sanger Institute + orcid: "https://orcid.org/0000-0002-8538-276X" - given-names: Priyanka family-names: Surana affiliation: Wellcome Sanger Institute orcid: "https://orcid.org/0000-0002-7167-0875" - - given-names: Yates - family-names: Bethan + - given-names: Bethan + family-names: Yates affiliation: Wellcome Sanger Institute orcid: "https://orcid.org/0000-0003-1658-1762" identifiers: @@ -34,5 +38,5 @@ identifiers: repository-code: "https://github.com/sanger-tol/genomenote" license: MIT commit: TODO -version: 1.2.1 +version: 1.2.2 date-released: "2022-10-07" diff --git a/conf/modules.config b/conf/modules.config index 5f7a2f61..ec011e2f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -50,7 +50,8 @@ process { } withName: BUSCO { - scratch = true + // Obey "use_work_dir_as_temp", except for large genomes + scratch = { !params.use_work_dir_as_temp || (meta.genome_size < 2000000000) } ext.args = { 'test' in workflow.profile.tokenize(',') ? // Additional configuration to speed processes up during testing. // Note: BUSCO *must* see the double-quotes around the parameters diff --git a/nextflow.config b/nextflow.config index 9cfa62ec..828ee20b 100644 --- a/nextflow.config +++ b/nextflow.config @@ -222,7 +222,7 @@ manifest { description = """Creating standarised genome assembly publications""" mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' - version = '1.2.1' + version = '1.2.2' doi = '10.5281/zenodo.7949384' }