Citations and Changelog

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 +64,27 @@ 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

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"

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
 
-<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  sanger-tol/curationpretext for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+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.
 

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