v5.2.1

Changed

• Updated epi2melabs to v0.0.56 to allow schemas without a demo_url field.

v5.2.0

Added

• Support for CRAM alignment format when creating IGV config files.
• Support for an optional "analysis_groups" column in the sample sheet providing grouping information for the input samples.

Changed

• Basecall models are now obtained from FASTQ / BAM input files via fastcat / bamstats output and added to sample meta map.

v5.1.4

Added

• Support for creating IGV JSON config files.

Changed

• Updated ezcharts to v0.9.1, showing coverage and accuracy plots when available.

v5.1.3

Changed

• workflow-glue CLI bootstrapping amended to skip imports of all components when not required.

v5.1.2

Added

• xam_ingress reads basecall_model and runid to metamap from RG DS tags.

v5.1.1

Fixed

• xam_ingress failing on BAM files that are lacking a @HD line in the header.

v5.1.0

Added

• Functionality to allow chunking of fastq outputs from ingress. Additional keys in meta information are added to reflect this.

Changed

• Use 4 threads for bgzip compressions during fastcat process.
• Updated fastcat to v0.17.0 for faster decompression and on-the-fly run ID summary.
• Updated to use ezCharts v0.8.0 for report generation.
• Remove per-read stats from fastcat output by default.

Fixed

• Ingress code would return stats even when not requested.

v5.0.4

Fixed

• xam_ingress failing to stage S3 BAM indexes.

v5.0.3

Changed

• Bumped wf-common to sha645176f98b8780851f9c476a064d44c2ae76ddf6.

Fixed

• Refusing to parse valid sample sheet CSV files in certain cases.

v5.0.2

Changed

• Bumped wf-common to sha362c808b4f22ce66f940bef192a1316aec5f4c75.