add descriptions of report files in tower.yml and correct output docu…

…mentation

docs/output.md

@@ -125,7 +125,7 @@ If no parameters are specified, the default is applied.
 <summary>Output files</summary>
 
 - `arriba_visualisation/`
-  - `<sample>.pdf`
+  - `<sample>_combined_fusions_arriba_visualisation.pdf`
 
 </details>
 
@@ -149,7 +149,7 @@ If `--trim_fastp` is selected, [fastp](https://github.com/OpenGene/fastp) will f
 <details markdown="1">
 <summary>Output files</summary>
 
-- `fastp`
+- `fastp/`
   - `<sample>_1.fastp.fastq.gz`
   - `<sample>_2.fastp.fastq.gz`
   - `<sample>.fastp.html`
@@ -245,7 +245,7 @@ Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or
 <summary>Output files</summary>
 
 - `megafusion`
-  - `<sample>.vcf` - contains the fusions in vcf format with collected statistics.
+  - `<sample>_fusion_data.vcf` - contains the fusions in vcf format with collected statistics.
 
 </details>
 
@@ -275,8 +275,8 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
 Picard CollectRnaMetrics and picard MarkDuplicates share the same output directory.
 
 - `picard`
-  - `<sample>.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics
-  - `<sample>_rna_metrics.txt` - metrics from MarkDuplicates
+  - `<sample>.MarkDuplicates.metrics.txt` - metrics from MarkDuplicates
+  - `<sample>_rna_metrics.txt` - metrics from CollectRnaMetrics
   - `<sample>.bam` - BAM file with marked duplicates
 
 </details>
@@ -462,6 +462,7 @@ For `STAR-fusion` with the parameters:
 
 - `<sample>.Aligned.sortedByCoord.out.bam`
 - `<sample>.Chimeric.out.junction`
+- `<sample>.ReadsPerGene.out.tab`
 
 </details>
 
@@ -474,8 +475,7 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par
 
 - `starfusion`
   - `<sample>.starfusion.fusion_predictions.tsv` - contains the identified fusions
-  - `<sample>.starfusion.abridged.tsv`
-  - `- contains the identified fusions.starfusion.abridged.coding_effect.tsv`
+  - `<sample>.starfusion.abridged.tsv`- contains the identified fusions.- `starfusion.abridged.coding_effect.tsv`
 
 </details>
 

tower.yml

@@ -1,5 +1,35 @@
 reports:
   multiqc_report.html:
     display: "MultiQC HTML report"
-  samplesheet.csv:
-    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
+  "**/arriba/*.arriba.fusions.tsv":
+    display: "Arriba identified fusion TSV report"
+  "**/arriba_visualisation/*_combined_fusions_arriba_visualisation.pdf":
+    display: "PDF visualisation of the transcripts involved in predicted fusions"
+  "**/fastp/*fastp.html":
+    display: "Post fastp trimming HTML report"
+  "**/fusioncatcher/*.fusioncatcher.fusion-genes.txt":
+    display: "FusionCatcher identified fusion TXT report"
+  "**/fusioninspector/*.FusionInspector.fusions.abridged.tsv":
+    display: "FusionInspector TSV report"
+  "**/fusionreport/*/*_fusionreport_index.html":
+    display: "Fusion-report HTML report"
+  "**/megafusion/*_fusion_data.vcf":
+    display: "Collected statistics on each fusion fed to FusionInspector in VCF format"
+  "**/picard/*.MarkDuplicates.metrics.txt":
+    display: "Picard: Metrics from CollectRnaMetrics"
+  "**/picard/*_rna_metrics.txt":
+    display: "Picard: Metrics from MarkDuplicates"
+  "**/pizzly/*.pizzly.txt":
+    display: "Pizzly identified fusion TXT report"
+  "**/qualimap/qualimapReport.html":
+    display: "Qualimap HTML report from STAR_FOR_STARFUSION alignment"
+  "**/qualimap/rnaseq_qc_results.txt":
+    display: "Qualimap QC results from STAR_FOR_STARFUSION alignment in TXT format"
+  "**/squid/*.squid.fusions.annotated.txt":
+    display: "Squid identified fusion TXT report"
+  "**/star_for_starfusion/*ReadsPerGene.out.tab":
+    display: "Number of reads per gene"
+  "**/starfusion/*.starfusion.fusion_predictions.tsv":
+    display: "STAR-Fusion identified fusion TSV report"
+  "**/stringtie/*/*stringtie.merged.gtf":
+    display: "Merged GTFs from StringTie with annotations"