lrp_4.0.39

Made MarkDuplicates optional to enable Amplicon data processing. (#486)

lrp_4.0.38

Updated python version in git actions from 3.7 to 3.13 (#487)

• Updated python version in git actions from 3.7 to 3.13

• Update python setup action version from 2 to 4

• Update python setup action version from 4 to 5

• Install libbz2-dev in deps

• Added additional deps in "Install dependencies"

• update tox py version from py37 to 313

• created separate step for system deps, added step to make sure miniconda is installed, added cache for pip deps

• removed miniconda step, replaced the system dep installation step

• Added system deps and pip caching to cd.yml

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Co-authored-by: bshifaw [email protected]

lrp_4.0.37

Fixed typo in zarr output file. (#484)

• Made zarr output file optional

lrp_4.0.36

Made zarr conversion optional in SRJointCallGVCFsWithGenomicsDB.wdl (#483)

lrp_4.0.35

Added snpeff_db_identifier for Functional annotation. (#482)

• Removed hard-coded plasmodium snpeff database specification.
• Added new input snpeff_db_identifier for a snpeff database
  specification to SRJointCallGVCFsWithGenomicsDB and
  FunctionalAnnotation`

lrp_4.0.34

Reserved more non-heap memory for the JVM when calling HaplotypeCaller (#481)

• Updated HaplotypeCaller task to reserve 20% or 4gb of memory for off-heap use (whichever is larger). This prevents out of memory errors occurring in native libraries that HaplotypeCaller calls into (i.e. the GKL).

lrp_4.0.33

SRJointCallGVCFsWithGenomicsDB.wdl now prefers dbsnp_vcf to known_sites_vcf for genotyping (#480)

• Added ResolveMapKeysInPriorityOrder to resolve keys in a WDL Map object in priority order. This enables fallbacks / preferences for different entries in a map (such as the refmap).
• For genotyping with the gnarly genotyper, the dbsnp resource now prefers dbsnp_vcf from the RefMap. If this does not exist, it will fall back to known_sites_vcf. This allows different resources to be used for BQSR (which prefers known_sites_vcf in SRFlowcell) and the gnarly genotyper, which now prefers dbsnp_vcf.

lrp_4.0.32

Updated SRUtils.BamToFq and SRBamToFq with cram support and better memory / cpu settings (#479)

• Made finalization optional in SRBamToFq.
• Now BamToFq sorts and converts in 2 separate commands.
• Now BamToFq utilizes all available processors.
• BamToFq cpu and ram now 8 cores and 16gb respectively.

lrp_4.0.31

Fixed unbound variable error in some cases of QC failure. (#478)

• When $mosdepth_qc_status was true and $callable_status was false, there
  was a bug that caused an unbound variable exception (message had not
  been defined in that code path).

lrp_4.0.30

Fixed bug when workflow had no inputs/outputs. (#477)

• Fixed the bug where if a workflow had no inputs or outputs the backup
  process would fail due to a python KeyError.