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Add population map with unassigned specimens and intermediate test files #2295

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9c220c5
Add population map with unassigned specimens
kathrynmurie Oct 1, 2026
c871f23
Add line describing unassigned specimens to readme
kathrynmurie Oct 1, 2026
e6de18f
Add intermediate files for tests
kathrynmurie Oct 1, 2026
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14 changes: 14 additions & 0 deletions README.md
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Expand Up @@ -15,3 +15,17 @@ The PMO file also contains synthetic sample metadata.
- `testdata/allele_table.tsv`: Microhaplotype allele table (`specimen_name`, `target_name`, `reads`, `seq`, plus optional `bioinformatics_run_name` / `allele` columns from the drugres extract).
- `testdata/population_assignment.tsv`: Specimen-to-population map (`specimen_name`, `population`) for optional `--population_map` runs.
- `testdata/example_PMO.json`: Example Portable Microhaplotype Object for `--pmo` / `-profile test_pmo`.
- `testdata/population_assignment_unassigned.tsv`: Specimen-to-population assignment table missing some specimens (`Vietnam2018-23`, `Vietnam2018-24`) to test handling of unassigned specimens.

### Module test inputs

Intermediate files produced by running the pipeline on `allele_table.tsv` with `population_assignment.tsv` (naive COI). Used as inputs to the module nf-tests.

- `testdata/population_map_indexed.tsv`: Indexed population map (`specimen_name`, `population`, `population_index`) from `INDEX_POPULATION_ASSIGNMENT`.
- `testdata/population_index_lookup.tsv`: Population index to population label lookup from `INDEX_POPULATION_ASSIGNMENT`.
- `testdata/popidx_001.allele_table.tsv.gz`: Allele table for one population from `SPLIT_ALLELE_TABLE_BY_POP`.
- `testdata/popidx_001.coi_table.tsv`: Naive COI table from `ESTIMATE_COI_NAIVE`.
- `testdata/popidx_001.naive.coi_table.tsv`: Standardised COI table from `STANDARDIZE_COI_TABLE`.
- `testdata/popidx_001.naive.coi_table.labeled.tsv`, `testdata/popidx_002.naive.coi_table.labeled.tsv`: COI tables with a population column from `ADD_POPULATION_COLUMN`.
- `testdata/popidx_001.allele_summary_by_target.tsv`: Per-locus allele summary from `ALLELE_PER_LOCUS_SUMMARY`.
- `testdata/popidx_001.per_locus_popgen_summary.tsv`: Per-locus popgen summary from `PER_LOCUS_POPGEN_SUMMARY`.
7 changes: 7 additions & 0 deletions testdata/popidx_001.allele_summary_by_target.tsv
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target_name total_allele_count unique_allele_count allele_singlets
Pf3D7_04_v3-0748128-0748326 3 2 1
Pf3D7_04_v3-0748406-0748581 3 2 1
Pf3D7_07_v3-0403499-0403683 3 2 1
Pf3D7_07_v3-0403507-0403717 3 2 1
Pf3D7_08_v3-0549609-0549776 3 2 1
Pf3D7_13_v3-1725493-1725694 2 1 0
Binary file added testdata/popidx_001.allele_table.tsv.gz
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3 changes: 3 additions & 0 deletions testdata/popidx_001.coi_table.tsv
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specimen_name coi
Laos2017-07 1
Laos2017-21 2
3 changes: 3 additions & 0 deletions testdata/popidx_001.naive.coi_table.labeled.tsv
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population coi_method specimen_name coi
Laos_201701-01 naive Laos2017-07 1
Laos_201701-01 naive Laos2017-21 2
3 changes: 3 additions & 0 deletions testdata/popidx_001.naive.coi_table.tsv
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coi_method specimen_name coi
naive Laos2017-07 1
naive Laos2017-21 2
7 changes: 7 additions & 0 deletions testdata/popidx_001.per_locus_popgen_summary.tsv
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target_name nucleotide_diversity segregating_sites tajima_d tajima_d_pval_normal tajima_d_pval_beta
Pf3D7_04_v3-0748128-0748326 0.0033670033670033673 1 NA NA NA
Pf3D7_04_v3-0748406-0748581 0.0038095238095238095 1 NA NA NA
Pf3D7_07_v3-0403499-0403683 0.0036231884057971015 1 NA NA NA
Pf3D7_07_v3-0403507-0403717 0.003174603174603175 1 NA NA NA
Pf3D7_08_v3-0549609-0549776 0.007984031936127746 2 NA NA NA
Pf3D7_13_v3-1725493-1725694 0 0 0 NA NA
3 changes: 3 additions & 0 deletions testdata/popidx_002.naive.coi_table.labeled.tsv
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population coi_method specimen_name coi
Vietnam_201701-01 naive Vietnam2017-07 1
Vietnam_201701-01 naive Vietnam2017-18 1
9 changes: 9 additions & 0 deletions testdata/population_assignment_unassigned.tsv
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specimen_name population
Vietnam2017-18 Vietnam_201701-01
Vietnam2018-25 Vietnam_201801-01
Laos2017-07 Laos_201701-01
Laos2017-21 Laos_201701-01
Vietnam2017-07 Vietnam_201701-01
Vietnam2018-15 Vietnam_201801-01
Vietnam2018-18 Vietnam_201801-01
Vietnam2018-21 Vietnam_201801-01
4 changes: 4 additions & 0 deletions testdata/population_index_lookup.tsv
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population_index population
popidx_001 Laos_201701-01
popidx_002 Vietnam_201701-01
popidx_003 Vietnam_201801-01
11 changes: 11 additions & 0 deletions testdata/population_map_indexed.tsv
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specimen_name population population_index
Vietnam2018-23 Vietnam_201801-01 popidx_003
Vietnam2018-24 Vietnam_201801-01 popidx_003
Vietnam2017-18 Vietnam_201701-01 popidx_002
Vietnam2018-25 Vietnam_201801-01 popidx_003
Laos2017-07 Laos_201701-01 popidx_001
Laos2017-21 Laos_201701-01 popidx_001
Vietnam2017-07 Vietnam_201701-01 popidx_002
Vietnam2018-15 Vietnam_201801-01 popidx_003
Vietnam2018-18 Vietnam_201801-01 popidx_003
Vietnam2018-21 Vietnam_201801-01 popidx_003
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