v5.3.1

Changed

• Datamodel-codegen now uses subclasses in Enum classes.

v5.3.0

Fixed

• Collections of sorted XAM files eligible for merge will no longer be needlessly re-sorted before merge.

Added

• reheader_samstream script to be used to restore a XAM header when aligning a XAM with the samtools bam2fq->minimap2 idiom.

Changed

• Supported multiple variation files for a single XAM file in configure_igv.

v5.2.6

Changed

• Updated wf-common to shad28e55140f75a68f59bbecc74e880aeab16ab158 improving legends and hovers for ezCharts plots (v0.11.2).

v5.2.5

Changed

• Updated wf-common to shae58638742cf84dbeeec683ba24bcdee67f64b986 fixing SeqSummary and SeqCompare plots in ezCharts (v0.11.0).

v5.2.4

Added

• meta keys src_xam and src_xai pointing to the input XAM/XAI files.
• src_xam and src_xai will be set to null if multiple XAM per sample are provided, if files are hosted in S3 or if the files are altered by ingress.nf.

Changed

• Updated wf-common to sha4a766a8333dbb72086b117c6eefba08e8ef7d76e to improve report layouts in EPI2ME Desktop with ezCharts (v0.10.2).
• Compare only SQ SN,LN,M5 when determining if collection of XAM headers have been aligned to conflicting references.
• Automatically emit the igv.json file upon generation.

Fixed

• Resumed workflow leading to mismatched (BAM, BAI) validateIndex pairs when calling xam_ingress more than once.
• Broken Markdown rendering of install and run section of README in desktop application.

v5.2.3

Changed

• Updated wf-common image to shad399cf22079b5b153920ac39ee40095a677933f1 to include latest fastcat (v0.18.6).

v5.2.2

Changed

• Matching RG.IDs found in XAM headers are now combined across all input XAM for a particular sample and emitted once, instead of emitting new RG.IDs for each XAM file.
• Bumped wf-common to shab540ba556d0d8c38bea8fec520f0bdedd9e59520.

Fixed

• Non-determinstic catting and merging of XAM files during ingress.

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.