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<https://github.com/nf-core/test-datasets/pull/1894|#1894 Add RAD-seq BAM test data for stacks/refmap module>
Pull request opened by <https://github.com/TheGreatJack|TheGreatJack>
*Summary*

Adding RAD-seq BAM test data for a `stacks/refmap` nf-core module that i plan to submit for publishing in the March 2026 Hackaton (<https://github.com/TheGreatJack/modules/tree/stacks-dev/modules/nf-core/stacks/refmap|Repo with the module>). I would like to have the data ready before the hackaton. You can checkout the stacks <https://catchenlab.life.illinois.edu/stacks/|suite here>.There is currently no RAD-seq BAM data in the `modules` branch.

*Data*

• *Organism:* _Limulus polyphemus_ (horseshoe crab), chromosome 26 ddRAD data
• *Source:* FASTQs from the existing `radseq` branch of this repo (msp_0 through msp_9), aligned to the reference genome using BWA
• *Files added* under `data/genomics/eukaryotes/limulus_polyphemus/radseq/`:  
   • `bwa_output/msp_0.bam` ... `msp_9.bam` (10 files, ~6KB each)  
   • `popmap.tsv` (2 populations: V1, V2)

*Testing*

I have tested this data locally with `ref_map.pl` from Stacks 2.68 and confirmed it runs successfully, producing all expected outputs (catalog, gstacks, populations stats, VCF, genepop, structure).

*Note*

I have used LLM assistance to move and organize files , everything has been double checked manually by me.
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>

Review on #1894 Add RAD-seq BAM test data for stacks/refmap module
Review comment by <https://github.com/jfy133|jfy133> on <https://github.com/TheGreatJack|TheGreatJack's> pull request
Please add entries for all the files on how they were generated/sourced from (so people know how to recreate/what's inside, if necessary) to the main README of the branch, and then I think you are good to go :)
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>

Review on #1894 Add RAD-seq BAM test data for stacks/refmap module
Review approved by <https://github.com/jfy133|jfy133> on <https://github.com/TheGreatJack|TheGreatJack's> pull request
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>

<https://github.com/nf-core/test-datasets/pull/1894|#1894 Add RAD-seq BAM test data for stacks/refmap module>
Pull request merged by <https://github.com/TheGreatJack|TheGreatJack>
<https://github.com/nf-core/test-datasets|nf-core/test-datasets>