From 2416620e950fa37fab77ee702ccb1c51f6d18eba Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Wed, 16 Sep 2026 06:52:09 -0700 Subject: [PATCH 1/5] Add eupathpopgen test data shared from plasmodiumdrugres. Reuse the drugres allele table and population assignment so related PlasmoGenEpi pipelines exercise the same inputs. Co-authored-by: Cursor --- README.md | 42 ++++++------------ testdata/allele_table.tsv | 70 ++++++++++++++++++++++++++++++ testdata/population_assignment.tsv | 11 +++++ 3 files changed, 95 insertions(+), 28 deletions(-) create mode 100644 testdata/allele_table.tsv create mode 100644 testdata/population_assignment.tsv diff --git a/README.md b/README.md index fb12179ae..7a8eb291a 100644 --- a/README.md +++ b/README.md @@ -1,39 +1,25 @@ -# ![nfcore/test-datasets](docs/images/test-datasets_logo.png) +# test-datasets: `eupathpopgen` -Test data to be used for automated testing with the nf-core pipelines +This branch contains test data for automated testing with the [nf-core/eupathpopgen](https://github.com/nf-core/eupathpopgen) pipeline (currently developed at [PlasmoGenEpi/eupathpopgen](https://github.com/PlasmoGenEpi/eupathpopgen)). -> ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)** +## Content of this repository -## Introduction +All files live under `testdata/`. These are the same simulated microhaplotype inputs used by [nf-core/plasmodiumdrugres](https://github.com/nf-core/plasmodiumdrugres) (shared from the `plasmodiumdrugres` test-datasets branch) so related PlasmoGenEpi pipelines stay consistent. -nf-core is a collection of high quality Nextflow pipelines. This repository contains various files for CI and unit testing of nf-core pipelines and infrastructure. +### Pipeline inputs -The principle for nf-core test data is as small as possible, as large as necessary. Please see the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines) for more detailed information. Always ask for guidance on the [nf-core slack](https://nf-co.re/join) before adding new test data. +- `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. -## Documentation - -nf-core/test-datasets comes with documentation in the `docs/` directory: - -1. [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md) -2. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md) - -## Downloading test data - -Due the large number of large files in this repository for each pipeline, we highly recommend cloning only the branches you would use. +## Usage ```bash -git clone --single-branch --branch +nextflow run nf-core/eupathpopgen \ + -profile test,docker \ + --outdir results ``` -To subsequently clone other branches[^1] - -```bash -git remote set-branches --add origin [remote-branch] -git fetch -``` - -## Support - -For further information or help, don't hesitate to get in touch on our [Slack organisation](https://nf-co.re/join/slack) (a tool for instant messaging). +Raw URLs (branch `eupathpopgen`): -[^1]: From [stackoverflow](https://stackoverflow.com/a/60846265/11502856) +- `https://raw.githubusercontent.com/nf-core/test-datasets/eupathpopgen/testdata/allele_table.tsv` +- `https://raw.githubusercontent.com/nf-core/test-datasets/eupathpopgen/testdata/population_assignment.tsv` diff --git a/testdata/allele_table.tsv b/testdata/allele_table.tsv new file mode 100644 index 000000000..80a0bbd60 --- /dev/null +++ b/testdata/allele_table.tsv @@ -0,0 +1,70 @@ +bioinformatics_run_name specimen_name target_name allele reads seq +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_13_v3-1725493-1725694 0 5046 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_08_v3-0549609-0549776 2 5199 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCGCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_04_v3-0748128-0748326 0 4795 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_07_v3-0403499-0403683 0 5240 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_04_v3-0748406-0748581 1 5210 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-25 Pf3D7_07_v3-0403507-0403717 0 5256 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_13_v3-1725493-1725694 0 5325 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_08_v3-0549609-0549776 0 5360 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_04_v3-0748128-0748326 0 4945 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_07_v3-0403499-0403683 0 4762 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_04_v3-0748406-0748581 0 4098 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-24 Pf3D7_07_v3-0403507-0403717 0 5251 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_13_v3-1725493-1725694 0 4557 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_08_v3-0549609-0549776 0 4398 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_04_v3-0748128-0748326 0 4547 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_07_v3-0403499-0403683 1 5074 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_04_v3-0748406-0748581 0 3908 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-07 Pf3D7_07_v3-0403507-0403717 1 4607 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_13_v3-1725493-1725694 0 5859 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_08_v3-0549609-0549776 0 5311 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_04_v3-0748128-0748326 0 4408 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_07_v3-0403499-0403683 0 5115 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_04_v3-0748406-0748581 0 4551 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-23 Pf3D7_07_v3-0403507-0403717 0 5277 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_13_v3-1725493-1725694 0 4635 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_08_v3-0549609-0549776 0 5177 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_04_v3-0748128-0748326 0 5061 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_07_v3-0403499-0403683 0 4490 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_07_v3-0403499-0403683 1 378 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_04_v3-0748406-0748581 1 5327 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_07_v3-0403507-0403717 0 5245 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-21 Pf3D7_07_v3-0403507-0403717 1 447 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_13_v3-1725493-1725694 0 5986 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_08_v3-0549609-0549776 0 5569 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_04_v3-0748128-0748326 0 5481 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_07_v3-0403499-0403683 0 4483 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_07_v3-0403499-0403683 1 596 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_04_v3-0748406-0748581 0 5073 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_07_v3-0403507-0403717 0 3523 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-18 Pf3D7_07_v3-0403507-0403717 1 502 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_13_v3-1725493-1725694 0 5765 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_08_v3-0549609-0549776 0 4121 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_04_v3-0748128-0748326 0 5788 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_07_v3-0403499-0403683 0 4592 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_04_v3-0748406-0748581 0 5747 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2017-18 Pf3D7_07_v3-0403507-0403717 4 5855 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTTACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_13_v3-1725493-1725694 0 5082 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_08_v3-0549609-0549776 0 4815 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_04_v3-0748128-0748326 0 4517 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_07_v3-0403499-0403683 0 5138 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_04_v3-0748406-0748581 1 4307 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG +ReducedMAD4HATTERSim-SeekDeep Vietnam2018-15 Pf3D7_07_v3-0403507-0403717 0 5787 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_13_v3-1725493-1725694 0 4717 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_08_v3-0549609-0549776 2 4233 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCGCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_04_v3-0748128-0748326 0 5160 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_07_v3-0403499-0403683 0 5449 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_04_v3-0748406-0748581 1 4879 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG +ReducedMAD4HATTERSim-SeekDeep Laos2017-07 Pf3D7_07_v3-0403507-0403717 0 4399 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_13_v3-1725493-1725694 0 4236 AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_08_v3-0549609-0549776 1 4451 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGCTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_08_v3-0549609-0549776 2 142 AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCGCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_04_v3-0748128-0748326 1 4612 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTAATTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_04_v3-0748128-0748326 0 157 ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_07_v3-0403499-0403683 2 4655 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGATACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_07_v3-0403499-0403683 0 139 TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_04_v3-0748406-0748581 1 5032 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_04_v3-0748406-0748581 0 172 CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_07_v3-0403507-0403717 2 4368 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGATACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA +ReducedMAD4HATTERSim-SeekDeep Laos2017-21 Pf3D7_07_v3-0403507-0403717 0 137 GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA diff --git a/testdata/population_assignment.tsv b/testdata/population_assignment.tsv new file mode 100644 index 000000000..4c78f1db4 --- /dev/null +++ b/testdata/population_assignment.tsv @@ -0,0 +1,11 @@ +specimen_name population +Vietnam2018-23 Vietnam_201801-01 +Vietnam2018-24 Vietnam_201801-01 +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 From 2520445e6f9a8887c84f4a2e2ccd33c6eb29df57 Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Wed, 16 Sep 2026 07:23:07 -0700 Subject: [PATCH 2/5] remove unnecessary info --- README.md | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/README.md b/README.md index 7a8eb291a..a7f2f90c6 100644 --- a/README.md +++ b/README.md @@ -1,25 +1,12 @@ # test-datasets: `eupathpopgen` -This branch contains test data for automated testing with the [nf-core/eupathpopgen](https://github.com/nf-core/eupathpopgen) pipeline (currently developed at [PlasmoGenEpi/eupathpopgen](https://github.com/PlasmoGenEpi/eupathpopgen)). +This branch contains test data for automated testing with the [nf-core/eupathpopgen](https://github.com/nf-core/eupathpopgen) pipeline. ## Content of this repository -All files live under `testdata/`. These are the same simulated microhaplotype inputs used by [nf-core/plasmodiumdrugres](https://github.com/nf-core/plasmodiumdrugres) (shared from the `plasmodiumdrugres` test-datasets branch) so related PlasmoGenEpi pipelines stay consistent. - +All files live under `testdata/` ### Pipeline inputs -- `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/allele_table.tsv`: Microhaplotype allele table (`specimen_name`, `target_name`, `reads`, `seq`, plus optional `bioinformatics_run_name`). - `testdata/population_assignment.tsv`: Specimen-to-population map (`specimen_name`, `population`) for optional `--population_map` runs. -## Usage - -```bash -nextflow run nf-core/eupathpopgen \ - -profile test,docker \ - --outdir results -``` - -Raw URLs (branch `eupathpopgen`): - -- `https://raw.githubusercontent.com/nf-core/test-datasets/eupathpopgen/testdata/allele_table.tsv` -- `https://raw.githubusercontent.com/nf-core/test-datasets/eupathpopgen/testdata/population_assignment.tsv` From 2a8a9508e024635b6f474eb5d1bfc96293f66d88 Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Wed, 16 Sep 2026 07:45:54 -0700 Subject: [PATCH 3/5] Add example pmo --- README.md | 7 +- testdata/example_PMO.json | 1251 +++++++++++++++++++++++++++++++++++++ 2 files changed, 1255 insertions(+), 3 deletions(-) create mode 100644 testdata/example_PMO.json diff --git a/README.md b/README.md index a7f2f90c6..e11a4d4fb 100644 --- a/README.md +++ b/README.md @@ -4,9 +4,10 @@ This branch contains test data for automated testing with the [nf-core/eupathpop ## Content of this repository -All files live under `testdata/` +All files live under `testdata/`. + ### Pipeline inputs -- `testdata/allele_table.tsv`: Microhaplotype allele table (`specimen_name`, `target_name`, `reads`, `seq`, plus optional `bioinformatics_run_name`). +- `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`. diff --git a/testdata/example_PMO.json b/testdata/example_PMO.json new file mode 100644 index 000000000..fecbb8175 --- /dev/null +++ b/testdata/example_PMO.json @@ -0,0 +1,1251 @@ +{ + "pmo_header": { + "creation_date": "2026-03-11", + "generation_method": { + "program_name": "elucidator combingallintopmojson", + "program_version": "1.1.1" + }, + "pmo_version": "v1.0.0" + }, + "panel_info": [ + { + "panel_name": "ReducedMAD4HATTER", + "reactions": [ + { + "reaction_name": "full", + "panel_targets": [0, 1, 2, 3, 4, 5] + } + ] + } + ], + "target_info": [ + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_13_v3", + "end": 1725493, + "genome_id": 0, + "start": 1725463, + "strand": "+" + }, + "seq": "CATACACCTCAGTTTCAAATAAAGCCTTAT" + }, + "gene_name": "PF3D7_1343700", + "insert_location": { + "chrom": "Pf3D7_13_v3", + "end": 1725694, + "genome_id": 0, + "ref_seq": "AATCATAGTTATTACCACCAAAAACGTATAAGAAATTATTCAATACAGCACTTCCAAAATAAGCTTTTTTGGTAGACATAGGTGTACACATACGCCAGCATTGTTGACTAATATCTAATAATTCCATCGAATTTAAATATTCTACACCATCAAATCCACCTATACAAAATACTAATGGGAATGGTAAAAATTTAATACCAT", + "start": 1725493, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_13_v3", + "end": 1725493, + "genome_id": 0, + "start": 1725463, + "strand": "+" + }, + "seq": "GCCTTGTTGAAAGAAGCAGAATTTT" + }, + "target_name": "Pf3D7_13_v3-1725493-1725694" + }, + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_08_v3", + "end": 549609, + "genome_id": 0, + "start": 549582, + "strand": "+" + }, + "seq": "CAGATGGAGGTATTTTTGTTGAACCTA" + }, + "gene_name": "PF3D7_0810800", + "insert_location": { + "chrom": "Pf3D7_08_v3", + "end": 549776, + "genome_id": 0, + "ref_seq": "AACGTGCTGTTCAAAGAATGTTTGAAATGATAAATGAAGGTGCTAGTGTTATAGATATAGGTGGAGAATCCTCTGGTCCTTTTGTTATACCTAATCCAAAAATTAGTGAAAGAGATTTAGTAGTACCTGTATTACAATTATTTCAAAAAGAATGGAATGATATAAAA", + "start": 549609, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_08_v3", + "end": 549609, + "genome_id": 0, + "start": 549582, + "strand": "+" + }, + "seq": "TTGGTTTCGCATCACATTTAACAATTTTATT" + }, + "target_name": "Pf3D7_08_v3-0549609-0549776" + }, + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_04_v3", + "end": 748128, + "genome_id": 0, + "start": 748104, + "strand": "+" + }, + "seq": "CGACGTTTTCGATATTTATGCCAT" + }, + "gene_name": "PF3D7_0417200", + "insert_location": { + "chrom": "Pf3D7_04_v3", + "end": 748326, + "genome_id": 0, + "ref_seq": "ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTAATTCCCTAGATATGAAATATTTTTGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA", + "start": 748128, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_04_v3", + "end": 748128, + "genome_id": 0, + "start": 748104, + "strand": "+" + }, + "seq": "TCATTTACATTATCCACAGTTTCTTTGTTTAAA" + }, + "target_name": "Pf3D7_04_v3-0748128-0748326" + }, + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_07_v3", + "end": 403499, + "genome_id": 0, + "start": 403478, + "strand": "+" + }, + "seq": "GACCTTAACAGATGGCTCACG" + }, + "gene_name": "PF3D7_0709000", + "insert_location": { + "chrom": "Pf3D7_07_v3", + "end": 403683, + "genome_id": 0, + "ref_seq": "TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATGAATAAAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA", + "start": 403499, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_07_v3", + "end": 403499, + "genome_id": 0, + "start": 403478, + "strand": "+" + }, + "seq": "AAAGAACATAATCATACAAATAAAGTTGTGAGT" + }, + "target_name": "Pf3D7_07_v3-0403499-0403683" + }, + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_04_v3", + "end": 748406, + "genome_id": 0, + "start": 748373, + "strand": "+" + }, + "seq": "AAAAATTACAAAATGTTGTAGTTATGGGAAGAA" + }, + "gene_name": "PF3D7_0417200", + "insert_location": { + "chrom": "Pf3D7_04_v3", + "end": 748581, + "genome_id": 0, + "ref_seq": "CAAGCTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG", + "start": 748406, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_04_v3", + "end": 748406, + "genome_id": 0, + "start": 748373, + "strand": "+" + }, + "seq": "TCTAAAAATTCTTGATAAACAACGGAACCT" + }, + "target_name": "Pf3D7_04_v3-0748406-0748581" + }, + { + "forward_primer": { + "location": { + "chrom": "Pf3D7_07_v3", + "end": 403507, + "genome_id": 0, + "start": 403486, + "strand": "+" + }, + "seq": "CAGATGGCTCACGTTTAGGTG" + }, + "gene_name": "PF3D7_0709000", + "insert_location": { + "chrom": "Pf3D7_07_v3", + "end": 403717, + "genome_id": 0, + "ref_seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATGAATAAAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA", + "start": 403507, + "strand": "+" + }, + "reverse_primer": { + "location": { + "chrom": "Pf3D7_07_v3", + "end": 403507, + "genome_id": 0, + "start": 403486, + "strand": "+" + }, + "seq": "TTCCCTTTTTATTTCCAAATAAGGAATAAACAA" + }, + "target_name": "Pf3D7_07_v3-0403507-0403717" + } + ], + "representative_microhaplotypes": { + "targets": [ + { + "mhap_location": { + "chrom": "Pf3D7_04_v3", + "end": 748326, + "genome_id": 0, + "start": 748128, + "strand": "+" + }, + "microhaplotypes": [ + { + "seq": "ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTATTTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA" + }, + { + "seq": "ATGTGCATGTTGTAAGGTTGAAAGCAAAAATGAGGGGAAAAAAAATGAGGTTTTTAATAACTACACATTTAGAGGTCTAGGAAATAAAGGAGTATTACCATGGAAATGTAATTCCCTAGATATGAAATATTTTCGTGCAGTTACAACATATGTGAATGAATCAAAATATGAAAAATTGAAATATAAGAGATGTAAATA" + } + ], + "target_id": 2 + }, + { + "mhap_location": { + "chrom": "Pf3D7_04_v3", + "end": 748581, + "genome_id": 0, + "start": 748406, + "strand": "+" + }, + "microhaplotypes": [ + { + "seq": "CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTTTAGG" + }, + { + "seq": "CAAACTGGGAAAGCATTCCAAAAAAATTTAAACCTTTAAGCAATAGGATAAATGTTATATTGTCTAGAACCTTAAAAAAAGAAGATTTTGATGAAGATGTTTATATCATTAACAAAGTTGAAGATCTAATAGTTTTACTTGGGAAATTAAATTACTATAAATGTTTTATTATAGG" + } + ], + "target_id": 4 + }, + { + "mhap_location": { + "chrom": "Pf3D7_07_v3", + "end": 403683, + "genome_id": 0, + "start": 403499, + "strand": "+" + }, + "microhaplotypes": [ + { + "seq": "TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA" + }, + { + "seq": "TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAA" + }, + { + "seq": "TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGATACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA" + }, + { + "seq": "TTTAGGTGGAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATGAATAAAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAA" + } + ], + "target_id": 3 + }, + { + "mhap_location": { + "chrom": "Pf3D7_07_v3", + "end": 403717, + "genome_id": 0, + "start": 403507, + "strand": "+" + }, + "microhaplotypes": [ + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA" + }, + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTATCATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA" + }, + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGATACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA" + }, + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCTCAACTTTATTTGTATGATTATGTTCTTTA" + }, + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATTGAAACAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTTACAACTTTATTTGTATGATTATGTTCTTTA" + }, + { + "seq": "GAGGTTCTTGTCTTGGTAAATGTGCTCATGTGTTTAAACTTATTTTTAAAGAGATTAAGGATAATATTTTTATTTATATTTTAAGTATTATTTATTTAAGTGTATGTGTAATGAATAAAATTTTTGCTAAAAGAACTTTAAACAAAATTGGTAACTATAGTTTTGTAACATCCGAAACTCACAACTTTATTTGTATGATTATGTTCTTTA" + } + ], + "target_id": 5 + }, + { + "mhap_location": { + "chrom": "Pf3D7_08_v3", + "end": 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"mhaps": [ + { + "mhap_id": 2, + "reads": 4368 + }, + { + "mhap_id": 0, + "reads": 137 + } + ], + "mhaps_target_id": 3 + } + ] + } + ], + "bioinformatics_run_id": 0 + } + ], + "sequencing_info": [ + { + "lib_kit": "TruSeq i5/i7 barcode primers", + "library_layout": "paired-end", + "library_selection": "RANDOM", + "library_source": "GENOMIC", + "library_strategy": "WGS", + "nucl_acid_date": "2024-01-10", + "pcr_cond": "simulated 23 rounds for density less than 6,000 and 45 rounds greater than 6,000", + "seq_center": "Nick computer", + "seq_date": "2024-01-10", + "seq_instrument_model": "NextSeq 550 simulated", + "seq_platform": "Illumina", + "sequencing_info_name": "ReducedMAD4HATTERSim" + } + ], + "project_info": [ + { + "project_collector_chief_scientist": "Nick Hathaway", + "project_description": "Simulation of MAD4HATTER panel", + "project_name": "ReducedMAD4HATTERSim" + } + ], + "bioinformatics_methods_info": [ + { + "methods": [ + { + "program": "SeekDeep extractorPairedEnd", + "program_description": "Takes raw paired-end reads and demultiplexes on primers and does QC filtering", + "program_version": "v2.6.5" + }, + { + "additional_argument": [ + "--illumina", + "--qualThres 25,20", + "--trimFront 1", + "--trimBack 1" + ], + "program": "SeekDeep qluster", + "program_description": "Takes sequences per sample per target and clusters them", + "program_version": "v2.6.5" + }, + { + "additional_argument": [ + "--strictErrors", + "--illumina", + "--removeOneSampOnlyOneOffHaps", + "--excludeCommonlyLowFreqHaplotypes", + "--excludeLowFreqOneOffs", + "--rescueExcludedOneOffLowFreqHaplotypes" + ], + "program": "SeekDeep processClusters", + "program_description": "Compare across samples for each target to create population level identifiers and do post artifact cleanup", + "program_version": "v2.6.5" + } + ] + } + ], + "bioinformatics_run_info": [ + { + "bioinformatics_methods_id": 0, + "bioinformatics_run_name": "ReducedMAD4HATTERSim-SeekDeep", + "run_date": "2025-01-11" + } + ], + "targeted_genomes": [ + { + "chromosomes": [ + "Pf3D7_01_v3", + "Pf3D7_02_v3", + "Pf3D7_03_v3", + "Pf3D7_04_v3", + "Pf3D7_05_v3", + "Pf3D7_06_v3", + "Pf3D7_07_v3", + "Pf3D7_08_v3", + "Pf3D7_09_v3", + "Pf3D7_10_v3", + "Pf3D7_11_v3", + "Pf3D7_12_v3", + "Pf3D7_13_v3", + "Pf3D7_14_v3", + "Pf3D7_API_v3", + "Pf3D7_MIT_v3" + ], + "genome_version": "2020-09-01", + "gff_url": "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/gff/data/PlasmoDB-65_Pfalciparum3D7.gff", + "name": "3D7", + "taxon_id": [5833], + "url": "https://plasmodb.org/common/downloads/release-65/Pfalciparum3D7/fasta/data/PlasmoDB-65_Pfalciparum3D7_Genome.fasta" + } + ], + "read_counts_by_stage": [] +} From 2191ad5b68e19d5d923d87e4e24f8098d6a59cd2 Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Mon, 28 Sep 2026 12:31:20 -0700 Subject: [PATCH 4/5] Add extra info about files to README --- README.md | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e11a4d4fb..24ee60f32 100644 --- a/README.md +++ b/README.md @@ -4,7 +4,13 @@ This branch contains test data for automated testing with the [nf-core/eupathpop ## Content of this repository -All files live under `testdata/`. + +All files are located under `testdata/`. The allele table and PMO examples represent the same dataset in different formats. + +The data were simulated using [recombuddy](https://github.com/PlasmoGenEpi/recombuddy) from a background population derived from publicly available whole-genome sequencing data from Southeast Asia (SEA). The simulated parasite genomes were then processed in silico using the MAD4HaTteR targeted sequencing panel to generate realistic targeted-sequencing FASTQ files. These FASTQ files were subsequently processed using the SeekDeep pipeline. + +The PMO file also contains synthetic sample metadata. + ### Pipeline inputs From 4573e48a49a32e54a0431d824451650547d823a9 Mon Sep 17 00:00:00 2001 From: kathryn1995 Date: Mon, 28 Sep 2026 12:33:07 -0700 Subject: [PATCH 5/5] Fix readme format --- README.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/README.md b/README.md index 24ee60f32..ca23796ed 100644 --- a/README.md +++ b/README.md @@ -4,13 +4,11 @@ This branch contains test data for automated testing with the [nf-core/eupathpop ## Content of this repository - All files are located under `testdata/`. The allele table and PMO examples represent the same dataset in different formats. The data were simulated using [recombuddy](https://github.com/PlasmoGenEpi/recombuddy) from a background population derived from publicly available whole-genome sequencing data from Southeast Asia (SEA). The simulated parasite genomes were then processed in silico using the MAD4HaTteR targeted sequencing panel to generate realistic targeted-sequencing FASTQ files. These FASTQ files were subsequently processed using the SeekDeep pipeline. The PMO file also contains synthetic sample metadata. - ### Pipeline inputs