Merge pull request #15 from sanger-tol/patch

Patch 2.0.1
sanger-tol · Dec 5, 2024 · 39b62c0 · 39b62c0
2 parents 5a8e597 + 851de96
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,23 @@
 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).
 
+## [[2.0.1](https://github.com/sanger-tol/ensemblgenedownload/releases/tag/2.0.1)] - Vicious Uruk-hai (patch 1) - [2024-12-05]
+
+### Enhancements & fixes
+
+- Update module versions
+- Remove reference to Anaconda repositories
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `Python`   | 3.8.3,3.9.1 | 3.9.1       |
+| `samtools` | 1.17        | 1.21        |
+| `tabix`    | 1.11        | 1.20        |
+
 ## [[2.0.0](https://github.com/sanger-tol/ensemblgenedownload/releases/tag/2.0.0)] – Vicious Uruk-hai – [2024-06-04]
 
 This version supports the new FTP structure of Ensembl
@@ -40,7 +57,7 @@ Note, since the pipeline is using Nextflow DSL2, each process will be run with i
 | ---------- | ----------- | ----------- |
 | multiqc    | 1.13        | 1.14        |
 
-## [[1.0.1](https://github.com/sanger-tol/ensemblgenedownload/releases/tag/1.0.1)] [2022-10-19]
+## [[1.0.1](https://github.com/sanger-tol/ensemblgenedownload/releases/tag/1.0.1)] – Hefty mûmakil (patch 1) – [2022-10-19]
 
 Minor bugfix update.
 

diff --git a/CITATION.cff b/CITATION.cff
@@ -16,6 +16,10 @@ authors:
       family-names: Surana
       orcid: "https://orcid.org/0000-0002-7167-0875"
       affiliation: Wellcome Sanger Institute
+    - given-names: Tyler
+      family-names: Chafin
+      orcid: "https://orcid.org/0000-0001-8687-5905"
+      affiliation: Wellcome Sanger Institute
 identifiers:
     - type: doi
       value: 10.5281/zenodo.7155206

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -20,9 +20,9 @@
 
 ## Software packaging/containerisation tools
 
-- [Anaconda](https://anaconda.com)
+- [Conda](https://conda.org/)
 
-  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+  > conda contributors. conda: A system-level, binary package and environment manager running on all major operating systems and platforms. Computer software. https://github.com/conda/conda
 
 - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7155206-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155206)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
-[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
+[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=conda)](https://docs.conda.io/en/latest/)
 [![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/)
 
@@ -62,6 +62,7 @@ sanger-tol/ensemblgenedownload was originally written by [Matthieu Muffato](http
 We thank the following people for their assistance in the development of this pipeline:
 
 - [Priyanka Surana](https://github.com/priyanka-surana) for providing reviews.
+- [Tyler Chafin](https://github.com/tkchafin) for updates and maintenance.
 
 ## Contributions and Support
 

diff --git a/modules.json b/modules.json
@@ -7,32 +7,32 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "49f4e50534fe4b64101e62ea41d5dc43b1324358",
                         "installed_by": ["modules"]
                     },
                     "samtools/dict": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgzip": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
@@ -3,10 +3,10 @@ process SAMPLESHEET_CHECK {
     tag "$samplesheet"
     label 'process_single'
 
-    conda "conda-forge::python=3.8.3"
+    conda "conda-forge::python=3.9.1"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/python:3.8.3' :
-        'biocontainers/python:3.8.3' }"
+        'https://depot.galaxyproject.org/singularity/python:3.9--1' :
+        'quay.io/biocontainers/python:3.9--1' }"
 
     input:
     path samplesheet

diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap
diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml
diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml
diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf