v1.1.11-himut.3 - Zhou Jichang (patch 3)

[1.1.11-himut.3] - Zhou Jichang (patch 3) - [2025-10-30]

Enhancements & fixes

• Moved away from the channel operator splitFasta as it creates memory issues (#135)

v1.1.10 - Shang Tang (patch 10)

[1.1.10] - Shang Tang (patch 10) - [2025-10-30]

Enhancements & fixes

• Fixed a bug introduced in 1.1.9 whereby only the first sample would be aligned

v1.1.9 - Shang Tang (patch 9)

[1.1.9] - Shang Tang (patch 9) - [2025-10-28]

Enhancements & fixes

• Moved away from the channel operator splitFasta as it creates memory issues (#135)

v1.1.9-himut.2 - Zhou Jichang (patch 2)

[1.1.9-himut.2] - Zhou Jichang (patch 2) - [2025-09-22]

Enhancements & fixes

• More memory for Himut

v1.1.9-himut.1 - Zhou Jichang

[1.1.9-himut.1] - Zhou Jichang - [2025-09-03]

Enhancements & fixes

• Add Himut module
• DeepVariant input change from cram/crai to bam/bai

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
Deepvariant	1.9.0	1.1.0
Himut		1.0.0

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

This release with the following initial parameters:

Old parameter	New parameter
	--assembly_report

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.

v1.1.8 - Shang Tang (patch 8)

[1.1.8] - Shang Tang (patch 8) - [2025-07-03]

Enhancements & fixes

• Fixed the bug of meta inputs in tabix module in subworkflow deepvariant_caller

v1.1.7 - Shang Tang (patch 7)

[1.1.7] - Shang Tang (patch 7) - [2025-06-26]

Enhancements & fixes

• Update Deepvariant to version 1.9.0 (conda-free)
• Add module DEEPVARIANT_VCFSTATSREPORT to generate visual report from Deepvariant
• Compress and index concatenated VCFs

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
Deepvariant	1.6.1	1.9.0
HTSlib		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.

v1.1.6 - Shang Tang (patch 6)

[1.1.6] - Shang Tang (patch 6) - [2025-02-10]

Enhancements & fixes

• Allow DeepVariant and BCFtools to handle CSI files
• Deal with genomes >4GB in Minimap

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
nextflow	22.10.1	23.10.1

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.

v1.1.5- Shang Tang (patch 5)

Enhancements & fixes

• Fix bug in alignment subworkflow

v1.1.4 - Shang Tang (patch 4)

Enhancements & fixes

• Module updates and remove Anaconda references

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
bcftools	1.17	1.20
blastn	2.14.1	2.15.0
deepvariant	1.5.0	1.6.1
Python	3.8.3	3.9.1
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.