epi2me-labs/wf-transcriptomes: v2.0.1

This patch release of wf-transcriptomes handles an additional quantification failure edge case that was not observed before release, fixes issues encountered by users during joint discovery when providing many samples, and makes some improvements to the volcano plot in the output report. Users of wf-transcriptomes v2.0.0 who have encountered issues during discovery and quantification should adopt this release.

Fixed

• "Error in full_join" encountered during runPerSampleBambuQuant when all read classes have no compatible transcript assignment. An empty quant table is correctly emitted instead.
• "unable to find an inherited method for function 'rowData'" encountered during runJointBambuDiscover when providing many samples. The workflow now correctly handles data spilled to disk by bambu discover.
• Fatal memory error (exit 137) encountered during collateBambuQuant when providing many samples with a large reference. Collation now uses a two-pass approach to process the per-chunk RDS results to avoid exhausting memory limits.
• Volcano plot class counts incorrect when log2FoldChange or padj columns contained NA values.
• IGV track not correctly loading in EPI2ME Desktop when a sample consists of a single input BAM.

Added

• Volcano plots now display the full y-axis range and include a slider to control the y-axis range maximum, which can be useful to exclude low p-value outliers.

Changed

• Adjusted p-values below 0.001 in the volcano selection table were rounded to 0.000, these are now shown in scientific notation.