v5.3.4

Changed

• Updated wf-common to shaabceef445fb63214073cbf5836fdd33c04be4ac7 to update ezcharts 0.11.5.

v5.3.3

Fixed

• Fixed regression in handling empty FASTQ files by updating wf-common to shabadd33adae761be6f2d59c6ecfb44b19cf472cfc to use fastcat v0.20.0

v5.3.2

Changed

• Corrected permissions for non-executable workflow_glue files in bin/.
• Updated wf-common to shaf15f9d80aba72c20e3e71f84869619873a56b8af to improve the performance of bamstats as provided by fastcat v0.19.1.

Fixed

• getParams process cache can lead to incorrect parameter table in report if workflow is run with -resume under different conditions.

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.