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sanger-tol/insdcdownload: Changelog

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

[2.0.0] – Light elf – [2024-06-04]

This version supports the new FTP structure of Ensembl

Enhancements & fixes

  • The sample-sheet column species_dir is replaced with the outdir column which represents where the assembly and repeats are downloaded (in immediate sub-directories)
  • 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
  • --outdir is a mandatory parameter

Parameters

In the samplesheet

Old parameter New parameter
species_dir outdir

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

[1.1.0] – Deciduous ent – [2022-10-07]

Minor update that fixes a few bugs

Fixed

  • BED files were not tabix-indexed with the right settings
  • Fasta files now have the .fa extension, rather than .fasta

Added

  • New species_dir column to indicate where to download the files to

[1.0.0] – Flaming balrog – [2022-08-12]

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

Added

  • Download from the NCBI
  • Unmasking of the NCBI assembly
  • samtools faidx and samtools dict indices
  • BED file with the coordinates of the masked region

Dependencies

All dependencies are automatically fetched by Singularity.

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