v2.2.0 - German Doberman

Enhancements & fixes

• Update of the NF-core template to 3.5.1. #168 and #154
  • Implements NF-test for pipeline wide testing. #169
  • Updating the structure of the subworkflows folder.
• Addition of the GFASTATS module and config.
• Addition of GenescopeFK histogram plots and related data #181 #157.
• Support for CLI provided Busco lineage to override the NCBI auto generated one.
• Addition of the Ancestral Element Analysis (Annotation Ancestral) subworkflow
  • Refer to https://github.com/sanger-tol/busco_painter for more information about the tool and its configuration. That repository also contains a complete annotation table for Lepidoptera.
• Refactor of the CONTACT_MAPS subworkflow to support both/either HIGLASS or PRETEXT map generation #183.
  • Split the logic for either method into HIGLASS_GENERATION and PRETEXT_GENERATION.
  • Addition of select_contact_map to select higlass, pretext, both for generation.
• Addition of MerquryFK module and config.
• Addition of support for a single haplotype assembly sourced from the samplesheet.csv.
• Remove biosample_wgs as a required parameter.
• Added support for providing an API key to NCBI datasets.
• Added the blobtk_plot nf-core module.
  • This module creates plots via calls to the blobtoolkit server or local blobdir.
• Added the btk_location and btk_online_location to provide the path of the blobdir (local or remote). If not provided the module will be skipped.
• Dropped support for Conda until FastK is properly released there
• Updated BUSCO from 5.7.1 to 6.0.0
  • Updated GENOME_STATISTICS and ANNOTATION_STATISTICS to add new param for busco.
• Updated notes in ANNOTATION_STATISTICS

Parameters

Old parameter	New parameter
	--busco_lineage
	--select_contact_map
	--btk_location
	--btk_online_location
	--ancestral_table
	--ancestral_busco_lineage
	--annotation_set

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
gfastats		1.3.10
cat		2.3.4
genescopefk		1.2
fastk_histex		1.1.0
pretextmap		PM=0.1.9 PG=0.0.9 ST=1.21
pretextsnapshot		0.0.4
samtools/faidx		1.21
merquryfk		FK=38b07c2 MFK=1.1.2 R=4.42
buscopainter.py		1.0.1
plot_buscopainter.R		1.0.1
blobtk_plot		0.7.1
busco_busco	5.7.1	6.0.0
datasets	15.12.0	16.22.1
agat	1.4.0	1.4.2
MultiQC	1.25.1	1.32
samtools		1.21