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CHANGELOG.md

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sanger-tol/ensemblrepeatdownload: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[2.0.2] - Shadowfax the Planerider (patch 2) - [2024-12-09]

Enhancements & fixes

  • Remove defaults from lib/Utils.groovy

[2.0.1] - Shadowfax the Planerider (patch 1) - [2024-12-05]

Enhancements & fixes

  • Update module versions
  • Remove reference to Anaconda repositories
  • Remove defaults from lib/Utils.groovy

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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] – Shadowfax the Planerider – [2024-06-04]

This version supports the new FTP structure of Ensembl

Enhancements & fixes

  • Support for the updated directory structure of the Ensembl FTP
  • Relative paths in the sample-sheet are now evaluated from the --outdir parameter
  • Memory usage rules for samtools dict
  • Appropriate use of tabix's TBI and CSI indexing, depending on the sequence lengths
  • New command-line parameter (--annotation_method): required for accessing the files on the Ensembl FTP
  • --outdir is a mandatory parameter

Parameters

Old parameter New parameter
--annotation_method

In the samplesheet

Old parameter New parameter
species_dir outdir
annotation_method
assembly_name

NB: Parameter has been updated if both old and new parameter information is present.
NB: Parameter has been added if just the new parameter information is present.
NB: Parameter has been removed if new parameter information isn't present.

Software dependencies

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. 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

[1.0.0] – Gwaihir the Windlord – [2022-10-19]

Initial release of sanger-tol/ensemblrepeatdownload, created with the nf-core template.

Added

  • Download from Ensembl
  • samtools faidx and samtools dict indices for the masked genome
  • BED file with the coordinates of the masked region
  • samtools faidx and samtools dict indices for the annotation fastas
  • tabix index for the GFF3 file

Dependencies

All dependencies are automatically fetched by Singularity.

  • bgzip
  • samtools
  • tabix
  • python3
  • wget
  • awk
  • gzip