Merge branch 'bokehreport_CW-3077' into 'dev'

Update report CW-3077

See merge request epi2melabs/workflows/wf-transcriptomes!168

CHANGELOG.md

@@ -4,6 +4,14 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+### Updated
+- Workflow report updated to use `ezcharts`.
+### Fixed
+- Exons per isoforms histogram reporting incorrect numbers.
+### Removed
+- per-class gffcompare tracking files as there exists a combine tracking file. 
+
 ## [v1.4.0]
 ## Added
 - `--igv` parameter (default: false) for outputting IGV config allowing visualisation of read alignments in the EPI2ME App.

README.md

@@ -210,13 +210,13 @@ Output files may be aggregated including information for all samples or provided
 | Title | File path | Description | Per sample or aggregated |
 |-------|-----------|-------------|--------------------------|
 | workflow report | wf-transcriptomes-report.html | a HTML report document detailing the primary findings of the workflow | aggregated |
-| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
-| Read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
-| Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
-| Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
-| Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
-| Assembled transcriptome | {{ alias }}_transcriptome.fas | Per sample assembled transcriptome. | per-sample |
-| Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample |
+| Per file read stats | fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-file-stats.tsv | A TSV with per file read stats, including all samples. | aggregated |
+| Read stats | fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
+| Run ID's | fastq_ingress_results/{{ alias }}//reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
+| Meta map json | fastq_ingress_results/{{ alias }}//reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
+| Concatenated sequence data | fastq_ingress_results/{{ alias }}//reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
+| Assembled transcriptome | {{ alias }}_transcriptome.fas | Per sample assembled transcriptome.  Not output if a reference annotation was supplied | per-sample |
+| Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. Only output if a reference annotation was supplied | per-sample |
 | Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample |
 | GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample |
 | Differential gene expression results | de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions. | aggregated |