Release/11.0.0

[jemten]

This PR adds | fixes:

• Updates MIP to version 11.0.0

Changelog

• HmtNote: annotate mitochondrial variants in VCF file
• Updating to latest and greatest versions
• Mitochondrial deletion analysis
• GATK Haplotypecaller has been turned off in favour of Deepvariant
• Introduces possibility to store singularity images locally as a .sif file
• Increased allele frequency cut off for when a variant is filtered out to 0.7

Tools

• cyrius v1.1 -> v1.1.1
• deepvariant 1.1.0-gpu -> 1.1.0
• deeptrio 1.1.0-gpu -> 1.1.0
• gatk 4.2.0.0 -> 4.2.2.0
• glnexus v1.3.1 -> v1.4.1
• HmtNote: 0.7.2
• htslib: 1.10.2 -> 1.13
• multiqc 1.10.1 -> v1.11
• star-fusion 1.10.0 -> 1.10.1
• vep release_103.1 -> release_104.3

References

• gnomad: r3.0 -> r3.1.1
• [NEW] gnomad mt: r3.1
• clinvar: 20210415 -> 20210919

How to test:

• Automatic and continuous test suite
• Install and run NIST samples with RTG recipe activated

Expected outcome:

• Installation, unit and integration test suite pass
• Run of NIST samples completes without errors (attach screenshot)
• No drop in sensitivity and specificity (attach screenshot)

Review:

• Code review
• Tests pass

This version is a:

• MAJOR - when you make incompatible API changes. If applicable record manual test results in PR header
• MINOR - when you add functionality in a backwards compatible manner. If applicable record manual test results in PR header
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

[jemten]

@ramprasadn and @henrikstranneheim could you please OK the PR :)

[ramprasadn]

LGTM 👍🏻