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CHANGELOG.md

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sanger-tol/genomenote: Changelog

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

[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

[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

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

Enhancements & fixes

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

[1.2.0] - Pyrenean Mountain Dog - [2024-05-01]

Enhancements & fixes

  • Updated the MerquryFK resources to cope with mistletoe (the pipeline as a whole is not yet fully compatible with mistletoe, though).
  • Updated the Busco resources to better deal with large genomes.
  • Round the chromosome lengths to 2 decimal points.
  • The pipeline is now publishing the Busco output directories.
  • The pipeline now generates a contact map for each Hi-C sample (instead of randomly picking one) and reports them all in the CSV.
  • The Hi-C contact map is now ordered according to the karyotype (as defined in the assembly record) by default, and added the --cool_order option to override it.

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.

Dependency Old version New version
busco 5.4.3 5.5.0

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.

Parameters

Old parameter New parameter
--cool_order

[1.1.2] - Golden Retriever (patch 2) - [2024-04-29]

Enhancements & fixes

  • Bugfix: the BAM still needs to be filtered with -F0x400

[1.1.1] - Golden Retriever (patch 1) - [2024-02-26]

Enhancements & fixes

  • Stopped forcing the eutheria_odb10 BUSCO lineage to be used for all mammals. This to synchronise this pipeline with the BlobToolKit pipeline.

[1.1.0] - Golden Retriever - [2024-01-04]

Enhancements & fixes

  • The pipeline now queries the NCBI Taxonomy API rather than GoaT to establish the list of lineages on which to run BUSCO. The possible lineages are now defined in the pipeline configuration but can be overridden with the --lineage_tax_ids parameter.
  • The pipeline will now immediately fail if the assembly can't be retrieve by the datasets command-line tool.
  • Pipeline information is now outputted in pipeline_info/genomenote/ instead of genomenote_info/.
  • maxRetries increased to 5 to cope with large datasets.
  • BUSCO now runs in "scratch" mode, i.e. off a temporary directory, as the number of files it creates could otherwise overwhelm a network filesystem.
  • SORT, FASTK, and MERQURYFK, can now put their temporary files in the work directory rather than /tmp. Turn that on with the --use_work_dir_as_temp flag.
  • The memory requirement of SORT is adjusted to account for some overheads and avoid the job to be killed.
  • All resource requirements (memory, time, CPUs) now fit the actual usage. This is achieved by automatically adjusting to the size of the input whenever possible.
  • Genomes with sequences longer than 2 Gbp are now supported thanks to upgrading FastK and MerquryFK.
  • Fixed a bug that was causing the Completeness to be reported as 0 in the statistics CSV file, when the k-mer database was constructed from BAM files.
  • QV/Completeness can now be computed off 10X sequencing data.
  • Minimal version of Nextflow downgraded to 23.04 to 22.10. 22.10 is tested as part of our continuous integration (CI) pipeline.
  • The "test" profile now runs faster, thanks to tuning some Busco/Metaeuk parameters.
  • The "test_full" profile is now tested automatically when updating the dev and main branches.
  • The pipelines now support Hi-C alignment files in the BAM format.

Parameters

Old parameter New parameter
--lineage_tax_ids
--use_work_dir_as_temp

Software dependencies

Dependency Old version New version
datasets 14.2 15.12
FastK f18a4e6d2207539f7b84461daebc54530a9559b0 427104ea91c78c3b8b8b49f1a7d6bbeaa869ba1c
MerquryFK 8ae344092df5dcaf83cfb7f90f662597a9b1fc61 d00d98157618f4e8d1a9190026b19b471055b22e

[1.0.0] - Czechoslovakian Wolfdog - [2023-05-18]

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

Enhancements & fixes

  • Created with nf-core/tools template v2.8.0.
  • Subworkflow to create HiC contact maps using Cooler.
  • Subworkflow to create summary table using BUSCO, MerquryFK, NCBI datasets, and Samtools.

Parameters

Old parameter New parameter
--input
--binsize
--kmer_size
--lineage_db
--fasta

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.

Dependency Old version New version
bedtools 2.30.0
busco 5.4.3
cooler 0.8.11
fastk f18a4e6d2207539f7b84461daebc54530a9559b0
merquryfk 8ae344092df5dcaf83cfb7f90f662597a9b1fc61
ncbi-datasets-cli 14.2.2
Nextflow 23.04.0
nf-core/tools 2.8.0
R 4.2.0
samtools 1.17

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.