HTML report/nfcore addons

README.md

@@ -110,16 +110,25 @@ RNA publishes:
 - `rna_split_fastqs/`
 - `rna_align/`
 - `TrES_Stats/`
+- `qc/samtools/`
+- `multiqc/`
+- `tres_report/`
 - `pipeline_info/`
 
 DNA publishes:
 
 - `dna_split_fastqs/`
 - `dna_align/`
 - `TrES_Stats/`
+- `qc/samtools/`
+- `multiqc/`
+- `tres_report/`
 - `pipeline_info/`
 
-`TrES_Stats/` includes RNA and DNA sequencing-efficiency UpSet PDF plots. Sankey plots, HTML reports, count tables, combined RNA+DNA reports, and sequencing-efficiency warning TSVs are not produced. Optional unavailable BAM-derived categories are skipped with warnings in the process log.
+The pipeline also writes two end-of-run HTML reports:
+
+- `tres_report/tres_report.html`: compact TrESFlow-specific RNA/DNA mapping and barcode summary
+- `multiqc/multiqc_report.html`: nf-core MultiQC aggregation of supported logs and QC files
 
 ## Runtime Contract
 
@@ -162,7 +171,7 @@ Default local CPU budget:
 
 Work-directory cleanup is intentionally aggressive: `--cleanup_work true` uses Nextflow's successful-run cleanup to remove task work directories after outputs have been published and downstream tasks have completed. This substantially reduces retained `work/` storage, but cleaned tasks are not expected to be usable with `--resume`. Set `--cleanup_work false` when you need the previous resume-friendly behavior for debugging or iterative development.
 
-DNA alignment no longer removes low-count cell barcodes during `ALIGN_DNA`. The aligned BAM still keeps proper-pair mapped, non-blacklisted reads; duplicate removal is represented later by `*_NoDup.bam`, and duplicate status appears in DNA sequencing-efficiency plots as `Unique +`.
+DNA alignment no longer removes low-count cell barcodes during `ALIGN_DNA`. The aligned BAM still keeps proper-pair mapped, non-blacklisted reads; duplicate removal is represented later by `*_NoDup.bam`.
 
 Every run writes:
 
@@ -171,6 +180,21 @@ Every run writes:
 - `${outdir}/pipeline_info/execution_trace.tsv`
 - `${outdir}/pipeline_info/flowchart.html`
 - `${outdir}/pipeline_info/runtime_contract.tsv`
+- `${outdir}/tres_report/tres_report.html` with per-library main statistics, detailed QC tables, and CSV/Excel export buttons
+- `${outdir}/tres_report/tres_report_metrics.json`
+- `${outdir}/multiqc/multiqc_report.html`
+
+Runs with real BAM outputs also write nf-core samtools sidecar QC under:
+
+- `${outdir}/qc/samtools/*.flagstat`
+- `${outdir}/qc/samtools/*.stats`
+- `${outdir}/qc/samtools/*.idxstats`
+- `${outdir}/qc/samtools/*.quickcheck.tsv`
+
+Raw FASTQ QC from nf-core FastQC is written under:
+
+- `${outdir}/qc/fastqc/*_fastqc.html`
+- `${outdir}/qc/fastqc/*_fastqc.zip`
 
 The active runtime scripts live under [`scripts/core_runtime/`](scripts/core_runtime/). `upstream/source_scripts/` is kept only as provenance for the vendored core code.
 

assets/test_realdata/ligation_barcode_whitelist.txt

@@ -0,0 +1,48 @@
+ATCACGTT
+CGATGTTT
+TTAGGCAT
+TGACCACT
+ACAGTGGT
+GCCAATGT
+CAGATCTG
+ACTTGATG
+GATCAGCG
+TAGCTTGT
+GGCTACAG
+CTTGTACT
+TGGTTGTT
+TCTCGGTT
+TAAGCGTT
+TCCGTCTT
+TGTACCTT
+TTCTGTGT
+TCTGCTGT
+TTGGAGGT
+TCGAGCGT
+TGATACGT
+TGCATAGT
+TTGACTCT
+TGCGATCT
+TTCCTGCT
+TAGTGACT
+TACAGGAT
+TCCTCAAT
+TGTGGTTG
+TACTAGTC
+TTCCATTG
+TCGAAGTG
+TAACGCTG
+TTGGTATG
+TGAACTGG
+TACTTCGG
+TCTCACGG
+TCAGGAGG
+TAAGTTCG
+TCCAGTCG
+TGTATGCG
+TCATTGAG
+TGGCTCAG
+TATGCCAG
+TCAGATTC
+TAGTCTTG
+TTCAGCTC