Merge pull request #15 from sanger-tol/patch

Patch
sanger-tol · Dec 9, 2024 · 4e4bac1 · 4e4bac1
2 parents 21757b3 + 8a7908a
commit 4e4bac1
Show file tree

Hide file tree

Showing 46 changed files with 1,560 additions and 149 deletions.
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/ensemblrepeatdownload/releases/tag/2.0.1)] - Shadowfax the Planerider (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/ensemblrepeatdownload/releases/tag/2.0.0)] – Shadowfax the Planerider – [2024-06-04]
 
 This version supports the new FTP structure of Ensembl

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.7183379

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.7183379-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7183379)
 
 [![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/)
 
@@ -61,6 +61,7 @@ sanger-tol/ensemblrepeatdownload was originally written by [Matthieu Muffato](ht
 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.
 
 ## Contributions and Support
 

diff --git a/lib/Utils.groovy b/lib/Utils.groovy
@@ -22,7 +22,7 @@ class Utils {
 
         // Check that all channels are present
         // This channel list is ordered by required channel priority.
-        def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults']
+        def required_channels_in_order = ['conda-forge', 'bioconda']
         def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean
 
         // Check that they are in the right order

diff --git a/modules.json b/modules.json
@@ -7,7 +7,7 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "custom/getchromsizes": {
@@ -17,22 +17,22 @@
                     },
                     "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/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml
diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf
diff --git a/modules/nf-core/samtools/dict/meta.yml b/modules/nf-core/samtools/dict/meta.yml