sanger-tol · tkchafin · Dec 5, 2024 · Dec 2, 2024 · Dec 2, 2024 · Dec 2, 2024
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,27 +3,56 @@
 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).
 
-## v1.1.0 - [date]
+## [[1.1.0](https://github.com/sanger-tol/sequencecomposition/releases/tag/1.1.0)] – Polite Platyfish – [2024-12-05]
 
-### `Fixed`
+### Enhancements & fixes
 
-### `Added`
+- Upgrade to the version 2.8 of the nf-core template.
+- nf-core module updates to remove Anaconda references
+- Updated configuration of the GitHub CI to improve testing.
+- Simpler samplesheet format, with just the path to the Fasta file and the output directory.
 
-## v1.0.0 - [2022-10-08]
+### 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.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| htslib     |             | 1.20        |
+| MultiQC    | 1.13        | 1.20        |
+| Python     | 3.8.3,3.9   | 3.9.1       |
+| samtools   |             | 1.21        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
+
+## [[1.0.0](https://github.com/sanger-tol/sequencecomposition/releases/tag/1.0.0)] – Apophis – [2022-10-08]
 
 Initial release of sanger-tol/sequencecomposition, created with the [nf-core](https://nf-co.re/) template.
 
-### `Added`
+### Enhancements & fixes
 
 - Run `fasta_windows` on an assembly
 - Convert all outputs to TSV and bedGraph files
 - Index all output files with `tabix`
 
-### `Dependencies`
+### 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.
+
+| Dependency    | Old version | New version |
+| ------------- | ----------- | ----------- |
+| fasta_windows |             | 0.2.4       |
+| MultiQC       |             | 1.13        |
+| Python        |             | 3.8.3,3.9   |
+| tabix         |             | 1.11        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present. </br> **NB:** Dependency has been **added** if just the new version information is present. </br> **NB:** Dependency has been **removed** if version information isn't present.
 
-All dependencies are automatically fetched by Singularity.
+### Parameters
 
-- fasta_windows
-- bgzip
-- tabix
-- python3
+| Old parameter | New parameter        |
+| ------------- | -------------------- |
+|               | --input              |
+|               | --fasta              |
+|               | --window_size_info   |
+|               | --selected_fw_output |
diff --git 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/sequencecomposition v1.0.0 - Apophis
+title: sanger-tol/sequencecomposition
 message: >-
     If you use this software, please cite it using the
     metadata from this file.
@@ -16,11 +16,15 @@ 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.7155168
 repository-code: "https://github.com/sanger-tol/sequencecomposition"
 license: MIT
 commit: TODO
-version: 1.0.0
+version: 2.0.0
 date-released: "2022-10-08"
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/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2022-2023 Genome Research Ltd.
+Copyright (c) 2022-2024 Genome Research Ltd.
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7155168-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7155168)
 
 [![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/)
 
@@ -55,6 +55,7 @@ sanger-tol/sequencecomposition 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.
 
 ## 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"]
                     },
                     "fastawindows": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["modules"]
                     },
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "e06548bfa36ee31869b81041879dd6b3a83b1d57",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "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' :
+        '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