Add a Ribo-TISH fixture with colon-qualified TisType values - #2208
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FelixKrueger merged 2 commits intoAug 10, 2026
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Ribo-TISH qualifies its positional TisType after a colon (`Novel:CDSFrameOverlap`) when a secondary annotation is supplied with `-a`, which happens in extended-ORF mode. The existing sample1.ribotish.pred.txt predates that mode and contains only bare tokens, so no fixture exercises the qualified form. One row per distinct TisType that Ribo-TISH emits on the chr20 test data in extended-ORF mode: seven qualified and seven bare. Rows are verbatim tool output, unmodified.
pinin4fjords
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There's a README is this folder for detail on where the files come from, and a top-level README which has a file listing. Can you add something to both relating to this file please?
Adds a table row and a derivation section in the orf_predictions README, and a listing entry in the top-level README. Three standing claims stop being true with a sixth file in the directory, so they are amended rather than left behind a new row: the folder README described five files, one per caller, each sliced to header + 15 records. This file is a second Ribo-TISH fixture, and it is row-selected to cover every distinct TisType rather than head-sliced.
FelixKrueger
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Added in e2aaba9 -- a table row plus a derivation section in the orf_predictions README, and a listing entry in the top-level one. I also amended three claims that a sixth file falsified: the folder README said five files, one per caller, each sliced to header + 15 records, and this is a second Ribo-TISH fixture that is row-selected rather than head-sliced.
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Replaces the inline synthetic rows with genomics/homo_sapiens/riboseq_expression/orf_predictions/sample1.ribotish.extended.pred.txt, added in nf-core/test-datasets#2208, plus the chr20 GTF the other ribotish tests use. Real extended-mode output carries seven colon-qualified TisType values, not the four this test previously covered: 5'UTR:Known, 5'UTR:CDSFrameOverlap and Truncated:Known also occur. All seven resolve through the existing CLASS_TOKENS table, and the test now names each one, so the vocabulary is pinned by the fixture rather than by hand-written rows.
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Ribo-TISH qualifies its
TisTypeafter a colon (Novel:CDSFrameOverlap) when a secondary annotation is passed with-a, which happens in extended-ORF mode. The existingsample1.ribotish.pred.txtpredates that mode and holds only bare tokens, so nothing exercises the qualified form. This adds a second file rather than changing it. It keeps one row per distinctTisTypethe tool emits on the chr20 test data in that mode — seven qualified, seven bare — with the rows verbatim.Requested by @pinin4fjords on nf-core/modules#12613, which needs it to test the qualified form against real output.
Provenance and contents (AI-assisted)
Generated by running the nf-core/riboseq pipeline on its own chr20 test data with
--extended_orf_analysis true --skip_stringtie false, which is what supplies Ribo-TISH's-a. Taken from the pooledRIBOTISH_PREDICToutput; all 19 columns and the header are unchanged, all rows are chr20, and every row is byte-identical to the tool's output.TisTypeTisTypeNovel:CDSFrameOverlapAnnotated5'UTR:KnownTruncated5'UTR:CDSFrameOverlapExtended3'UTR:CDSFrameOverlapNovelTruncated:Known5'UTRNovel:Known3'UTRInternal:CDSFrameOverlapInternalThree of the qualified forms (
5'UTR:Known,5'UTR:CDSFrameOverlap,Truncated:Known) were not previously known to occur; they turned up only once real extended-mode output was inspected.