v2.0.2 -- Vicious Uruk-hai (patch 2)

Enhancements & fixes

• Remove defaults from lib/Utils.groovy

v2.0.1 - Vicious Uruk-hai (patch 1)

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. 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

v2.0.0 – Vicious Uruk-hai

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

v1.0.1 – Hefty mûmakil (patch 1)

Overview

The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions.
Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk.
The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file.
All files are compressed with bgzip, and indexed with samtools faidx or tabix.

Steps involved:

• Download from Ensembl the GFF3 file, and the sequences of the genes in
  Fasta format.
• Compress and index all Fasta files with bgzip, samtools faidx, and
  samtools dict.
• Compress and index the GFF3 file with bgzip and tabix.

Fixed since v1.0.0

When a samplesheet is provided, do not process the individual command-line parameters

Dependencies

All dependencies are automatically fetched by Singularity.

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

v1.0.0 – Hefty mûmakil

Overview

The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions.
Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk.
The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file.
All files are compressed with bgzip, and indexed with samtools faidx or tabix.

Steps involved:

• Download from Ensembl the GFF3 file, and the sequences of the genes in
  Fasta format.
• Compress and index all Fasta files with bgzip, samtools faidx, and
  samtools dict.
• Compress and index the GFF3 file with bgzip and tabix.

Dependencies

All dependencies are automatically fetched by Singularity.

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