Release-notes

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Release 1.1.3 – 2024-11-20

  • Updated default duet pipeline version to 1.4.1 in all install scripts
  • Fixed a problem when running the DMR calling workflow could in certain cases fail with a missing --dmr-bed-path parameter error.

Release 1.1.2 – 2024-11-11

  • Updated duet pipeline version to 1.4.1
  • Checking that all 3 biomodal scripts are referencing the same version
  • Fixed typo in FASTQ file names in the documentation

Release 1.1.1 – 2024-11-06

New functionality in 1.1.1

  • Introduced new D(h)MR calling workflow using biomodal call_dmr
  • Optional sharing of all events
  • Recommend duet resource profiles when running biomodal validate

Other updates in 1.1.1

  • Terraform module updates for AWS, GCP and Azure
  • Updated default duet pipeline to version 1.4.0
  • meta-file parameter is optional for the biomodal analyse command
  • Reduced the number of Docker containers for the duet pipeline
  • Added description and link to nf-core pipelines in the documentation

Release 1.1.0 – 2024-06-26

New functionality in 1.1.0

  • New pipeline to make bespoke genome references, version 1.0.1
    • reference pipeline list – list available reference pipeline versions
    • reference pipeline download – download new reference pipeline version
    • biomodal reference make – make new reference genomes for the duet pipeline
    • Optional --reference-genome-profile parameter for biomodal analyse command
  • Input validation biomodal validate command to validate all biomodal analyse parameters, files and directories
  • Nextflow HTML reports automatically generated for biomodal test and biomodal analyse commands

Other updates in 1.1.0

  • duet 1.3.0 pipeline as default version
  • duet 1.3.0 module requirements updated
  • updated password reset link to match new API endpoint in documentation
  • updated biomodal info to show basic HPC queue settings
  • Terraform module updates for AWS, GCP and Azure
  • Improved labelling strategy for cloud platforms
  • Introduced _biomodal_functions.sh sub-script
  • Introduced _biomodal_validate.sh sub-script
  • Recommentations for SGE/OGE/UGE HPC cluster that is not supporting h_rt, h_rss or mem_free settings
  • Cloud executor error strategy [0,10,14] retry for biomodal test and biomodal analyse commands

Release 1.0.5 – 2024-04-24

  • Default duet pipeline version updated to 1.2.1
  • duet error strategy tests for exit 14 (cloud premption) only
  • Documentation updates
    • GIAB download instructions updated
    • Guidance on FASTQ sequence ID format and usage

Release 1.0.4 – 2024-03-20

  • Default duet pipeline version updated to 1.2.0
  • Continuous Integration(CI) automation added for auth and init stages
  • Updated Nextflow version for all platforms
  • Check that duet is installed before running test and analyse commands
  • biomodal info shows singularity environment variables if present
  • Documentation updates
    • Update hardware requirements for duet pipeline 1.2.0 modules
    • Recommendation for nextflow queue settings
    • Instructions for analysing GIAB data
    • Added examples for analyse command

Release 1.0.3 – 2023-12-04

New functionality in 1.0.3

  • Targeted mode added as main parameters for biomodal analyse command

Parameter updates

  • Updated software dependency from pcregrep to pcre2grep
  • Added --work-dir as an optional parameter to the biomodal analyse command
  • Renamed install scripts to better reflect use cases:
    • bootstrap-tool -> biomodal-cloud-utils
    • bootstrap-on-hpc -> biomodal-hpc-utils-admin
    • bootstrap-on-hpc-nosudo -> biomodal-hpc-utils-conda
  • Added biomodal analyze as an alias to biomodal analyse
  • Added queueSize parameter to limit the number of parallel pipeline processes
  • Extended biomodal info command to provide additional information about the current installation

Cloud/HPC installation and running optimisation

  • Added check and warning for insufficient initial free disk space to HPC install scripts
  • Various HPC install scripts improvements and bug fixes
  • Updated software dependency validation for orchestrator and worker nodes respectively
  • Added Google SDK installation in biomodal-hpc-utils-conda
  • Updated Terraform modules for AWS and GCP
  • Replaced AWS bastion module for Terraform
  • Added test option for Cloud install scripts
  • Labels supported for Cloud platforms to enable resource cost tracking

Documentation updates

  • Show link to online documentation directly in multiple CLI commands
  • Restructured user documentation into sub-pages
  • Added further information on installing software as modules on HPC
  • Added LSF and SLURM scheduler recommendations
  • Added decision flowchart to select correct installation script and options
  • Added how to run the CLI as a HPC module
  • Updated pipeline module hardware resource recommendations
  • Amended new bootstrap/install script names
  • Variant Associated Methylation (VAM) introduction
  • Use of public IP on cloud bootstrapped VMs

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Release 1.0.2 – 2023-08-18

  • Added support and prompting for custom install locations for software components during installation
  • Updated Terraform modules for AWS, GCP and Azure
  • Improvements and bug fixes on non-admin install script bootstrap-on-hpc-nosudo
  • Removed software dependency on yq package
  • Updated dependent software module versions
  • Added support for Nextflow work-dir parameter
  • Fixed the use of --resume parameter in the CLI
  • Changed the mandatory requirement of the use of --additional-params parameter to optional
  • Formatted API messages in the CLI script
  • Updated documentation for HPC install
  • Updated biomodal info command coverage to display additional information about the current installation

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Release 1.0.1 – 2023-05-24

  • Added support for biomodal duet analysis pipeline v1.1.1

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Release 1.0.0 – 2023-05-22

  • First official release of the biomodal CLI, including installation scripts for AWS, GCP, Azure and HPC platforms.

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