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anaconda purge #23

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21 changes: 21 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,27 @@
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/insdcdownload/releases/tag/2.0.1)] - Light elf (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 |
| ---------- | ----------- | ----------- |
| multiqc | 1.13 | 1.14 |

| 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/insdcdownload/releases/tag/2.0.0)] – Light elf – [2024-06-04]

This version supports the new FTP structure of Ensembl
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4 changes: 4 additions & 0 deletions CITATION.cff
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Expand Up @@ -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.6983932
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4 changes: 2 additions & 2 deletions CITATIONS.md
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Expand Up @@ -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/)

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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -7,7 +7,7 @@
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.6983932-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.6983932)

[![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/)

Expand Down Expand Up @@ -61,6 +61,7 @@ sanger-tol/insdcdownload was mainly written by [Matthieu Muffato](https://github
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

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12 changes: 6 additions & 6 deletions modules.json
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Expand Up @@ -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"]
}
}
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6 changes: 3 additions & 3 deletions modules/local/samplesheet_check.nf
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Expand Up @@ -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
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5 changes: 5 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/environment.yml

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6 changes: 3 additions & 3 deletions modules/nf-core/custom/dumpsoftwareversions/main.nf

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43 changes: 25 additions & 18 deletions modules/nf-core/custom/dumpsoftwareversions/meta.yml

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43 changes: 43 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test

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2 changes: 2 additions & 0 deletions modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml

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7 changes: 7 additions & 0 deletions modules/nf-core/custom/getchromsizes/environment.yml

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9 changes: 6 additions & 3 deletions modules/nf-core/custom/getchromsizes/main.nf

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