v1.1.4

Changed

• Reconcile template with v5.3.0 and v5.3.1
• IGV output files are only output if --igv is used

v1.1.3

Fixed

• Automated basecaller detection failing in some circumstances.

Changed

• Updated Ezcharts to v0.11.2.

v1.1.2

Fixed

• The workflow failing in de novo mode when all reads for a sample came from the same strand.

Changed

• The report now skips read length histograms etc. if there were no reads left after filtering.

v1.1.1

Changed

• Updated Medaka to v1.12.0.

Removed

• The --medaka_model parameter as the appropriate Medaka model is now automatically determined from the input data.
• The now redundant --basecaller_cfg parameter as its value is now automatically detected from the input data on a per-sample basis.

Added

• --override_basecaller_cfg parameter for cases where automatic selection fails or users wishes to override the automatic choice.

v1.1.0

Fixed

• The miniasm process requesting too little memory in some cases.
• Spurious out-of-memory errors for the SPOA process.
• Variant calling mode with --combine_results failing with a single sample/barcode.

Changed

• When there is at least one amplicon depth plot that shows more than one sample, the depth plots now use consistent colours for individual samples across the different amplicons.
• The workflow now uses the fastcat read length and quality histograms instead of the per-read stats in the report process.

Added

• IGV config json file to the outputs (in order to visualise the alignments and called variants).

v1.0.4

Fixed

• The workflow failing when there were tab characters in the FASTA header lines of reference sequences.

Changed

• The way the reference sequence IDs are sanitised to prevent issues with special characters.

v1.0.3

Fixed

• The workflow failing when there was a whitespace in the name of the reference file.

Changed

• The report now consistently uses the sanitised reference sequence IDs throughout.
• Some formatting changes to github issue template.

v1.0.2

Fixed

• Incorrect CPU use specification for the medakaVariant process.

v1.0.1

Changed

• Default for --reads_downsampling_size to 1500 to limit memory usage.
• Default for --medaka_target_depth_per_strand to 150 as the workflow now supports longer amplicons.

Fixed

• The workflow failing when a sample had only a single read.

v1.0.0

Added

• Memory requirements for each process.

Changed

• Reworked docs to follow new layout.