nf-core · FelixKrueger · Aug 10, 2026 · Aug 9, 2026 · Aug 10, 2026
diff --git a/README.md b/README.md
@@ -500,6 +500,7 @@ The earth sciences folder contain subfolders for different data formats encounte
         - test_pre_config.txt: P-site configuration file output from ribocode/metaplots for testing ribocode/ribocode module
       - orf_predictions
         - sample1.ribocode.txt, sample1.ribotish.pred.txt, sample1.ribotricer.tsv, sample1.rpbp.predicted-orfs.bed.gz, cohort.price.orfs.tsv: Five real-tool ORF prediction outputs (one per Ribo-seq ORF caller) sliced to header + 15 records (<13 KB each). Used by custom/orfnormalise + custom/orfmerge tests. Per-fixture provenance, source-module-test details and slim recipes are in `orf_predictions/README.md`.
+        - sample1.ribotish.extended.pred.txt: Real Ribo-TISH output from a run given a secondary annotation (`-a`), where TisType values take a `<location>:<qualifier>` form such as `Novel:CDSFrameOverlap`. One row per distinct TisType, seven qualified and seven bare. Used by custom/orfnormalise to test that classification reads the location and preserves the full value in `orf_type_native`. Derivation in `orf_predictions/README.md`.
       - orf_catalogue
         - cohort.catalogue.bed12, cohort.catalogue.tsv, cohort.orf_to_gene.tsv, cohort.catalogue.mqc.tsv, cohort.catalogue.aa.fasta, cohort_cluster.tsv: A small hand-built merged ORF catalogue (orfmerge output shape) with a duplicate-peptide smORF pair on opposite strands, used by the custom/orfcollapse test to exercise amino-acid-level small-ORF deduplication (a case absent from the real chr20 data). Details in `orf_catalogue/README.md`.
       - salmon.merged.gene_counts_length_scaled.tsv: Example matrix containing both Riboseq and RNA-seq runs, suitable for translational efficiency analysis

diff --git a/data/genomics/homo_sapiens/riboseq_expression/orf_predictions/README.md b/data/genomics/homo_sapiens/riboseq_expression/orf_predictions/README.md
@@ -1,26 +1,32 @@
 # Test data for `custom/orfnormalise` + `custom/orfmerge`
 
-Five small per-caller Ribo-seq ORF prediction outputs (one per supported
-caller), used by `modules/nf-core/custom/orfnormalise` and
-`modules/nf-core/custom/orfmerge` to exercise the parser, classifier,
-score-direction, and cross-caller merge logic end-to-end.
+Six small Ribo-seq ORF prediction outputs — one per supported caller, plus a
+second Ribo-TISH file covering its extended-ORF output — used by
+`modules/nf-core/custom/orfnormalise` and `modules/nf-core/custom/orfmerge` to
+exercise the parser, classifier, score-direction, and cross-caller merge logic
+end-to-end.
 
 | File                                 | Size  | Caller     | Source genome |
 | ------------------------------------ | ----- | ---------- | ------------- |
 | `sample1.ribocode.txt`               | 13 KB | RiboCode   | chr20         |
 | `sample1.ribotish.pred.txt`          | 3 KB  | Ribo-TISH  | chr20         |
+| `sample1.ribotish.extended.pred.txt` | 3 KB  | Ribo-TISH  | chr20         |
 | `sample1.ribotricer.tsv`             | 3 KB  | Ribotricer | chr20         |
 | `sample1.rpbp.predicted-orfs.bed.gz` | 2 KB  | Rp-Bp      | chr20         |
 | `cohort.price.orfs.tsv`              | 5 KB  | PRICE      | chr19+chr22   |
 
-Each file is the head + first 15 records of a real-tool output, so every
-column the downstream parsers read is exercised; no synthetic data.
+All are real-tool output with no synthetic data. The first five are the head
+plus first 15 records, so every column the downstream parsers read is
+exercised; `sample1.ribotish.extended.pred.txt` is row-selected instead, to
+cover each distinct `TisType` value (see below).
 
 ## How they were derived
 
-All five files are sliced from outputs produced by existing nf-core/modules
+Five of the six are sliced from outputs produced by existing nf-core/modules
 tests (or nf-core/modules#11695 for Rp-Bp) on the VM, then trimmed to
-header + 15 records with `head`.
+header + 15 records with `head`. `sample1.ribotish.extended.pred.txt` comes
+from an nf-core/riboseq pipeline run instead, because no module test supplies
+the input that produces its ORF-type values.
 
 ### `sample1.ribocode.txt`
 
@@ -59,6 +65,41 @@ awk -F'\t' 'BEGIN{OFS="\t"} NR==1 {print; next} {if ($15=="None" && $13!="None")
     sample1.ribotish.pred.txt > .tmp && mv .tmp sample1.ribotish.pred.txt
 ```
 
+### `sample1.ribotish.extended.pred.txt`
+
+Ribo-TISH qualifies its `TisType` after a colon (`Novel:CDSFrameOverlap`) only
+when a secondary annotation is supplied with `-a`, which nf-core/riboseq does in
+extended-ORF mode. `sample1.ribotish.pred.txt` above predates that mode and its
+`ribotish/predict` test passes no secondary annotation, so no fixture carried a
+qualified value.
+
+Produced by running nf-core/riboseq on its own chr20 test data:
+
+```bash
+nextflow run nf-core/riboseq -profile test,docker \
+    --skip_stringtie false \
+    --extended_orf_analysis true \
+    --outdir results
+```
+
+Taken from the pooled Ribo-TISH output
+(`results/orf_predictions/ribotish_all/allsamples_pred.txt`, 2716 records) and
+reduced to one row per distinct `TisType` — seven qualified, seven bare:
+
+| Qualified                  | Bare        |
+| -------------------------- | ----------- |
+| `Novel:CDSFrameOverlap`    | `Annotated` |
+| `5'UTR:Known`              | `Truncated` |
+| `5'UTR:CDSFrameOverlap`    | `Extended`  |
+| `3'UTR:CDSFrameOverlap`    | `Novel`     |
+| `Truncated:Known`          | `5'UTR`     |
+| `Novel:Known`              | `3'UTR`     |
+| `Internal:CDSFrameOverlap` | `Internal`  |
+
+All 19 columns and the header are unchanged, every row is verbatim tool output,
+and all rows are chr20 with transcript and gene ids that resolve against
+`Homo_sapiens.GRCh38.111_chr20.gtf`.
+
 ### `sample1.ribotricer.tsv`
 
 Produced by `modules/nf-core/ribotricer/detectorfs` test against

diff --git a/...nomics/homo_sapiens/riboseq_expression/orf_predictions/sample1.ribotish.extended.pred.txt b/...nomics/homo_sapiens/riboseq_expression/orf_predictions/sample1.ribotish.extended.pred.txt
@@ -0,0 +1,15 @@
+Gid	Tid	Symbol	GeneType	GenomePos	StartCodon	Start	Stop	TisType	TISGroup	TISCounts	TISPvalue	RiboPvalue	RiboPStatus	FisherPvalue	TISQvalue	FrameQvalue	FisherQvalue	AALen
+ENSG00000088832	ENST00000677937	FKBP1A	protein_coding	20:1372111-1392903:-	ATG	135	447	Novel:CDSFrameOverlap	0	0	None	0.01045891220436919	T	None	None	0.008669308713579512	None	103
+ENSG00000125863	ENST00000347364	MKKS	protein_coding	20:10420545-10420737:-	ATG	136	328	5'UTR:Known	0	0	None	0.011162037836675912	T	None	None	0.009183430665627096	None	63
+ENSG00000125863	ENST00000347364	MKKS	protein_coding	20:10420545-10420692:-	ATG	181	328	5'UTR:CDSFrameOverlap	0	0	None	0.037141070338459446	N	None	None	0.024981455883948636	None	48
+ENSG00000289720	ENST00000696979		protein_coding	20:34534647-34540624:+	ATG	2972	3164	3'UTR:CDSFrameOverlap	0	0	None	0.004346450743587745	N	None	None	0.003999095572590074	None	63
+ENSG00000244005	ENST00000374092	NFS1	protein_coding	20:35669621-35674542:-	ATG	1087	1438	Truncated:Known	0	0	None	0.0006960307379439676	N	None	None	0.0007930992920145594	None	116
+ENSG00000101017	ENST00000695669	CD40	protein_coding	20:46118343-46123418:+	ATG	73	769	Novel:Known	0	0	None	0.006682042341578261	T	None	None	0.0057399520695824895	None	231
+ENSG00000026036	ENST00000492259	RTEL1-TNFRSF6B	protein_coding	20:63690293-63695785:+	ATG	2328	3723	Internal:CDSFrameOverlap	0	0	None	0.016524496926863717	T	None	None	0.012536556718583385	None	464
+ENSG00000196476	ENST00000360321	C20orf96	protein_coding	20:271206-290610:-	ATG	140	1232	Annotated	0	0	None	0.03998989937315105	N	None	None	0.02666494606566258	None	363
+ENSG00000196476	ENST00000360321	C20orf96	protein_coding	20:271206-289586:-	ATG	299	1232	Truncated	0	0	None	0.0399780718546241	T	None	None	0.02666494606566258	None	310
+ENSG00000215388	ENST00000431775	ACTG1P3	processed_pseudogene	20:1160583-1160901:+	ATG	0	318	Novel	0	0	None	0.04464398440956175	N	None	None	0.029305362590948902	None	105
+ENSG00000101224	ENST00000245960	CDC25B	protein_coding	20:3805975-3806113:+	ATG	2979	3117	3'UTR	0	0	None	0.04689458029515801	T	None	None	0.030714477600042533	None	46
+ENSG00000178726	ENST00000377103	THBD	protein_coding	20:23047776-23049672:-	ATG	0	1896	Extended	0	0	None	2.1818407880632916e-07	N	None	None	6.479738219826158e-07	None	631
+ENSG00000171552	ENST00000450273	BCL2L1	protein_coding	20:31722270-31723776:-	ATG	196	316	5'UTR	0	0	None	0.010557079266845102	T	None	None	0.008746589504727273	None	39
+ENSG00000124145	ENST00000372733	SDC4	protein_coding	20:45327205-45327334:-	ATG	566	695	Internal	0	0	None	0.02707341799961499	T	None	None	0.019624354093751996	None	42