v1.1.3 – Shang Tang(patch 3)

[1.1.3] - Shang Tang (patch 3) - [2024-05-24]

Enhancements & fixes

• Fixed the bug in the filtering of multiple PacBio files

v1.1.2 – Shang Tang(patch 2)

[1.1.2] - Shang Tang (patch 2) - [2024-03-14]

Summary of the release

Enhancements & fixes

• Bug fix when index fai file given for reference fasta file

Parameters

This release with the following initial parameters:

Old parameter	New parameter

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

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.

v1.1.1 – Shang Tang (patch 1)

[1.1.1] - Shang Tang (patch 1) - [2024-02-02]

Summary of the release

Enhancements & fixes

• Bug fix when reference fasta file name end with .fa or .fa.gz

Parameters

This release with the following initial parameters:

Old parameter	New parameter

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

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.

v1.1.0 – Shang Tang

[1.1.0] - Shang Tang - [2023-12-20]

Enhancements & fixes

• Updated the CI procedure to use "sanger-tol" rather than "nf-core" names.
• Renamed Sanger related Github CI test workflows.
• nf-core template was updated from 2.7 to 2.8.
• Removed BAM/CRAM index files from the sample sheets.
• Made fasta index file optional from the inputs.
• Imported PacBio readmapping sub-workflows from sanger-tol/readmapping pipeline. Therefore, the pipeline can run on unaligned BAM/CRAM samples now.
• Use VCFtools to calculate per site nucleotide diversity.
• Use VCFtools to calculate heterozygosity.

Parameters

This release with the following initial parameters:

Old parameter	New parameter
--gzi
	--vector_db
	--align
	--include_positions
	--exclude_positions

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
DeepVariant	1.4.0	1.5.0
samtools	1.16.1	1.17
bcftools	1.16.1	1.17
python	3.11.0	3.11.4
vcftools		0.1.16
blast		2.14.1+
gunzip:		1.10
minimap2		2.24-r1122
awk		5.1.0
untar		1.30

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.

v1.0.0 – Xia Yu

[1.0.0] - Xia Yu - [2023-05-03]

Initial release of sanger-tol/variantcalling, created with the nf-core tools.

Enhancements & fixes

• Created with nf-core template v2.7.2.
• Allows calling variants using DeepVariant for PacBio long read data.
• Significant speed improvements made by splitting the genome before calling variants.
• Outputs both vcf and gvcf formats.

Parameters

This release with the following initial parameters:

Old parameter	New parameter
	--input
	--fasta
	--fai
	--gzi
	--interval
	--split_fasta_cutoff

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
DeepVariant		1.4.0
samtools		1.16.1
bcftools		1.16.1
nextflow		22.10.6
python		3.11.0
python		3.8.3
pigz		2.3.4
yaml		6.0

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.