From 50c05e1fa2d1e6a8ed0e554ef0cb854cbfd13666 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 13 Dec 2024 16:13:00 +0000 Subject: [PATCH 1/2] Citations and Changelog --- CHANGELOG.md | 24 +++++++++++++++++++++++- CITATION.cff | 22 +++++----------------- README.md | 8 ++++++-- nextflow.config | 2 +- 4 files changed, 35 insertions(+), 21 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0a80aec..c65e72f 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -34,8 +34,8 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i | cram_filter_align_bwamem2_fixmate_sort | - | | | ^ ( samtools + bwamem2 ) ^ | 1.17 + 2.2.1 | - | | cram_filter_minimap2_filter5end_fixmate_sort | - | | -| custom_dumpsoftwareversions | - | Python 3.11.7 + yaml 5.4.1 | | ^ ( samtools + minimap2 ) ^ | 1.17 + 2.24 | - | +| custom_dumpsoftwareversions | - | Python 3.11.7 + yaml 5.4.1 | | extract_cov_id ( coreutils ) | 9.1 | 9.3 | | extract_repeat ( perl ) | 5.26.2 | - | | extract_telo ( coreutils ) | - | 9.1 | @@ -64,6 +64,28 @@ Even modules which have not had a version bump have indeed been updated through Some modules now have two versions, the new addition is the script version rather than just the dependency version. +## [[1.0.1](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.1)] - UNSC Cradle H1 - [2024-10-24] + +## Added + +- Ability for end users to select "sorted" or "unsorted" (default) for the pretext maps. +- Adds a container for find_telomere. + +### Paramters + +| Old Version | New Versions | +| ----------- | --------------- | +| | --map_order | + +### Software Dependencies + +No updates to dependency versions + +### Dependencies + +### Deprecated + + ## [[1.0.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0)] - UNSC Cradle - [2024-02-22] ### Added diff --git a/CITATION.cff b/CITATION.cff index 8a0ff1c..ae554a6 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -2,7 +2,7 @@ # Visit https://bit.ly/cffinit to generate yours today! cff-version: 1.2.0 -title: sanger-tol/curationpretext v1.0.0 +title: "sanger-tol/curationpretext" message: >- If you use this software, please cite it using the metadata from this file. @@ -12,23 +12,11 @@ authors: family-names: Pointon affiliation: Wellcome Sanger Institute orcid: "https://orcid.org/0000-0003-2949-6719" - - given-names: Matthieu - family-names: Muffato - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0002-7860-3560" - - given-names: Ying - family-names: Sims - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0000-0003-4765-4872" - - given-names: William - family-names: Eagles - affiliation: Wellcome Sanger Institute - orcid: "https://orcid.org/0009-0006-9956-0404" identifiers: - type: doi - value: 10.5281/zenodo.XXXXXXX + value: 10.5281/zenodo.12773958 repository-code: "https://github.com/sanger-tol/curationpretext" license: MIT -commit: TODO -version: 1.0.0 -date-released: "2024-07-18" +version: 1.1.0 +date-released: "2024-12-13" +url: "https://pipelines.tol.sanger.ac.uk/curationpretext" diff --git a/README.md b/README.md index c4771c1..244835c 100755 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ # ![sanger-tol/curationpretext](docs/images/curationpretext-light.png#gh-light-mode-only) ![sanger-tol/curationpretext](docs/images/curationpretext-dark.png#gh-dark-mode-only) +[![GitHub Actions CI Status](https://github.com/sanger-tol/curationpretext/workflows/nf-core%20CI/badge.svg)](https://github.com/sanger-tol/curationpretext/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/sanger-tol/curationpretext/workflows/nf-core%20linting/badge.svg)](https://github.com/sanger-tol/curationpretext/actions?query=workflow%3A%22nf-core+linting%22)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.12773958-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.12773958) + [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) @@ -111,6 +114,8 @@ sanger-tol/curationpretext was originally written by Damon-Lee B Pointon (@DLBPo We thank the following people for their extensive assistance in the development of this pipeline: +- @muffato - For reviews. + - @yumisims - TreeVal and Software. - @weaglesBio - TreeVal and Software. @@ -125,8 +130,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - +If you use sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.12773958](https://doi.org/10.5281/zenodo.12773958) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/nextflow.config b/nextflow.config index fae62fa..b6bc50b 100755 --- a/nextflow.config +++ b/nextflow.config @@ -204,7 +204,7 @@ manifest { mainScript = 'main.nf' nextflowVersion = '!>=22.10.1' version = '1.1.0' - doi = '' + doi = '10.5281/zenodo.12773958' } // Load modules.config for DSL2 module specific options From 6151b22fcc527bab2703fa6afafe0704b1715544 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Fri, 13 Dec 2024 16:16:01 +0000 Subject: [PATCH 2/2] Prettier linting --- CHANGELOG.md | 7 +++---- README.md | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c65e72f..ee00c43 100755 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -73,9 +73,9 @@ Some modules now have two versions, the new addition is the script version rathe ### Paramters -| Old Version | New Versions | -| ----------- | --------------- | -| | --map_order | +| Old Version | New Versions | +| ----------- | ------------ | +| | --map_order | ### Software Dependencies @@ -85,7 +85,6 @@ No updates to dependency versions ### Deprecated - ## [[1.0.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0)] - UNSC Cradle - [2024-02-22] ### Added diff --git a/README.md b/README.md index 244835c..4748a8b 100755 --- a/README.md +++ b/README.md @@ -130,7 +130,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations -If you use sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.12773958](https://doi.org/10.5281/zenodo.12773958) +If you use sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.12773958](https://doi.org/10.5281/zenodo.12773958) An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.