version 1.3.0

What's Changed

v1.3.0

Features

• Implementation of support for hg38 genome build (requires reinstalling conda environment or pulling latest docker image). Hg38 can now be used as the genome reference build by setting the appropriate config parameter.
• Implementation of CRAM file support by specifying the filetype and reference genome file config parameters. NB this functions by decompressing CRAMs to BAMs as Rsamtools (currently) does not support loading CRAM files by default. While the snakemake pipeline will remove BAMs once downstream files are generated, be aware of increased disk usage and batch snakemake jobs accordingly.

Other changes

• Bumped R version from 3.6.4 to 4.2.0 for package stability with hg38 reference
• Added additional documentation for newly supported features

Bugs resolved

issue #11

• Dev branch PR - v1.3.0 by @Phil9S in #27
  Full Changelog: v1.2.0...v1.3.0

version 1.2.0

What's Changed

version 1.2.0

Features

• config parameters to specify seed and seed value
• config parameters to toggle use of power calculation filtering on CN ploidy/purity combinations
• Final output includes a combined CN segment table
• Inclusion of pre-determined ploidy and purity minimum and maximum search spaces
• User provided ploidy and purity solutions and implementation of stage 1 skip if all samples have pre-computed ploidy and purity values
• Homozygous loss filter and config parameters

Other changes

• Default minimum purity changed from 0.05 to 0.15
• Added default_config.yaml file as reference
• Fixed schema filtering and error catching to only include acceptable parameters
• docker container & snakemake singularity support
• added additional documentation

Bugs resolved

• issue #22
• issue #23
• issue #24
• issue #25

Full Changelog: v1.1.2...v1.2.0

v1.1.2

What's Changed

• development branch - issue resolutions by @Phil9S in #19

Full Changelog: v1.1.1...v1.1.2

Release v1.1.1

Release v1.1.1

Features

• None

Additional

• None

Bugs resolved

• Resolved hard-coded TP53 bin index which prevented the selection of the correct TP53 bin at different bin sizes other than 30Kb as referenced in issue #9
• Restored slurm job submission scripts removed during previous commit as referenced in issue #8
• Added note to documentation regarding reference genome compatibility

v1.1.0

Release v1.1.0

Features

• Scatter-gather jobs across multiple bin size values
• Allele frequency anchoring threshold variable
• Additional cluster/server job submission profiles (local/pbs)

Additional

• Overhaul of internal script submission method by snakemake
• Reimplementation of job submission profiles for allow for rule-specific alterations and increased flexibility
• Some code refactoring for efficiency

Bugs resolved

#3 Poorly formed or empty bam files are now checked and the pipeline will exit if identified (though not elegantly)
#4 Alterations to sample_sheet.tsv no longer impact on-going runs
#6 Resolved in code base
#7 Pipeline now exits if sample_id is not unique

Initial release

Identical to v1.0.0 with extended documentation