Release v1.8.0

Changes

• Support for single sample through CLI parameters --input_name, --input_tumor_bam and --input_normal_bam

Release v1.7.0

Changes

• The GnomAD resource is now optional, in case it is not available or you don't trust how it is used. When --gnomad is not provided then the contamination estimation steps are skipped. Also the filtering of common germline mutations is disabled. As an alternative a contamination estimate can be provided through --args_filter "--contamination-estimate 0.2"

Release v1.6.0

Changes

• Upgrade GATK from 4.2.5.0 to 4.2.6.1

Release 1.5.0

Changes

• Integration of funcotator as an optional final step. Output in VCF and MAF formats
• Arguments parameter to Mutect2 --args_mutect2 and to FilterMutectCalls and --args_filter
• Additional --enable_bam_output parameter which outputs a BAM from Mutect2 with the reassembly results
• Upgraded GATK version from 4.2.0.0 to 4.2.5.0
• Added a more realistic test dataset
• Confusing CPIU parameters are removed

Release v1.4.0

Changes

• The RG:SM are now read from the BAM headers and hence any arbitrary value can be passed.
• Some sanity checks on the RG:SM tags are added

Release v1.3.0

Non functional changes

• Migrate workflow to DSL 2
• Make conda dependencies more granular
• Improve tests

Tronflow Mutect2 release v1.2.0

Changes:

• Memory and CPUs are now parametrised more granularily
• Analysis intervals are now optional
• Integrates GitHub CI to replace Gitlab CI in the future

TronFlow mutect2 v1.1.0

Changes:

• Fix issue pulling from repo
• Remove hard coded references

TronFlow mutect2 v1.0.0

Changes:

• Add support for replicates in Mutect2
• Improve tests to check output files

TronFlow mutect2 v0.3.1

Minor changes:

• Replace image copied from Mutect2 best practices by URL
• Added some bibliographic references in the README