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

1.2.6 - Pyrenean Mountain Dog (patch 6)

Enhancements & fixes

• Upgraded the versions of FastK and MerquryFK to address some segmentation-fault issues.
• Upgraded the version of the NCBI datasets CLI and implemented a retry-and-backoff strategy
  to avoid overwhelming the server.

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
datasets	15.12.0	16.22.1
fastk	1.2	ddea6cf254f378db51d22c6eb21af775fa9e1f77
merquryfk	1.2	4578fc778098859d78cab5e4b78b27b9a9dd10a4

v2.1.1 - Pembroke Welsh Corgi (patch 1)

Enhancements & fixes

• Call the /v2 version of the NCBI datasets API rather than /v2alpha
• Fixed a bug in FETCH_ENSEMBL_METADATA when the Ensembl API fails
• Fixed the runtime requirement of MultiQC

1.2.5 - Pyrenean Mountain Dog (patch 5)

Enhancements & fixes

• Moved over to the NCBI API v2 since the v1 is deprecated
• Fixed the process name for Busco

v2.1.0 - Pembroke Welsh Corgi

Enhancements & fixes

• New annotation_statistics subworkfow which runs BUSCO in protein mode and generates some basic statistics on the the annotated gene set if provided with a GFF3 file of gene annotations using the --annotation_set option.
• The genome_metadata subworkflow now queries Ensembl's GraphQL API to determine if Ensembl has released gene annotation for the assembly being processed.
• Module updates and remove Anaconda channels
• Removed merquryfk completeness metric

Parameters

Old parameter	New parameter
	--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
agat		1.4.0
bedtools	2.30.0	2.31.1
busco	5.5.0	5.7.1
cooler	0.8.11	0.9.2
fastk	427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c	666652151335353eef2fcd58880bcef5bc2928e1
gffread		0.12.7
merquryfk	d00d98157618f4e8d1a9190026b19b471055b22e
multiqc	1.14	1.25.1
samtools	1.17	1.21

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

v1.2.4 - Pyrenean Mountain Dog (patch 4)

Enhancements & fixes

• Remove defaults from lib/Utils.groovy

v.1.2.3 - Pyrenean Mountain Dog (patch 3)

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
bedtools	2.30.0	2.31.1
busco	5.5.0	5.7.1
cooler	0.8.11	0.9.2
fastk	1.0.1	1.2
merquryfk	1.0.1	1.2
multiqc	1.14	1.25.1
samtools	1.17	1.20

v2.0.0 - English Cocker Spaniel

[2.0.0] - English Cocker Spaniel [2024-10-10]

Enhancements & fixes

• New genome_metadata subworkflow to fetch metadata linked to the genome assembly from various sources (COPO, GoaT, GBIF, ENA, NCBI). The options --assembly, --biosample_wgs, --biosample_hic and --biosample_rna specify what metadata to fetch and process.
• Now outputs a partially completed genome note document based on a template file which contains placeholder parameters. These placeholders are replaced with data generated by the pipeline. The template file to use can be specified using the --note_template option.
• Added the --write_to_portal option to write a set of key-value data parameters to a Genome Notes database.
• Added the --upload_higlass_data option to automatically upload the Hi-C Map to a kubernetes hosted Hi-Glass server.
• Bugfix: don't rely on fasta file name to correctly set assembly accession needed for use with ncbi datasets.
• Bugfix: ensure meta.id is used consistently.

Parameters

Old parameter	New parameter
	--assembly
	--biosample_wgs
	--biosample_hic
	--biosample_rna
	--write_to_portal
	--genome_notes_api
	--note_template
	--upload_higlass_data
	--higlass_url
	--higlass_deployment_name
	--higlass_namespace
	--higlass_kubeconfig
	--higlass_upload_directory
	--higlass_data_project_dir

v1.2.2 – Pyrenean Mountain Dog (patch 2)

[1.2.2] - Pyrenean Mountain Dog (patch 2) - [2024-09-10]

Enhancements & fixes

• Bugfix: don't run Busco in scratch mode for large genomes as it takes too much space on /tmp

v1.2.1 – Pyrenean Mountain Dog (patch 1)

[1.2.1] - Pyrenean Mountain Dog (patch 1) - [2024-07-12]

Enhancements & fixes

• Bugfix: Now handles missing fields in ncbi datasets genome report