diff --git a/docs/output.md b/docs/output.md index bd611b97..4144891b 100644 --- a/docs/output.md +++ b/docs/output.md @@ -125,7 +125,7 @@ If no parameters are specified, the default is applied. Output files - `arriba_visualisation/` - - `.pdf` + - `_combined_fusions_arriba_visualisation.pdf` @@ -149,7 +149,7 @@ If `--trim_fastp` is selected, [fastp](https://github.com/OpenGene/fastp) will f
Output files -- `fastp` +- `fastp/` - `_1.fastp.fastq.gz` - `_2.fastp.fastq.gz` - `.fastp.html` @@ -245,7 +245,7 @@ Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or Output files - `megafusion` - - `.vcf` - contains the fusions in vcf format with collected statistics. + - `_fusion_data.vcf` - contains the fusions in vcf format with collected statistics.
@@ -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` - - `.MarkDuplicates.metrics.txt` - metrics from CollectRnaMetrics - - `_rna_metrics.txt` - metrics from MarkDuplicates + - `.MarkDuplicates.metrics.txt` - metrics from MarkDuplicates + - `_rna_metrics.txt` - metrics from CollectRnaMetrics - `.bam` - BAM file with marked duplicates @@ -462,6 +462,7 @@ For `STAR-fusion` with the parameters: - `.Aligned.sortedByCoord.out.bam` - `.Chimeric.out.junction` +- `.ReadsPerGene.out.tab` @@ -474,8 +475,8 @@ The STAR index is generated with `--sjdbOverhang ${params.read_length - 1}`, par - `starfusion` - `.starfusion.fusion_predictions.tsv` - contains the identified fusions - - `.starfusion.abridged.tsv` - - `- contains the identified fusions.starfusion.abridged.coding_effect.tsv` + - `.starfusion.abridged.tsv` - contains the identified fusions abridged + - `starfusion.abridged.coding_effect.tsv` diff --git a/tower.yml b/tower.yml index 787aedfe..5813f5d3 100644 --- a/tower.yml +++ b/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"