Hello, I have written a Nextflow module to support WormCat, a tool designed to help C. elegans researchers categorize and visualize gene set enrichment data. I am now working on the nf-test cases and need some advice on test data. I came across the nf-core test-datasets repository, but I was wondering whether it is acceptable to host my own test data or whether I should create a new branch in the nf-core/test-datasets repository. WormCat accepts CSV or Excel files as input. The CSV file must include a column header named

Sequence ID

or

Wormbase ID

(case-sensitive). Any advice would be appreciated. Thanks!

for modules, please use the

modules

branch. all test data for nf-core modules needs to be there

Hi everyone, @mashehu I'm preparing test data for an nf-core module and would appreciate some guidance on how best to organize and submit it to the

nf-core/test-datasets

repository. I've reviewed the nf-core module test data guidelines and browsed the existing directory structure in the `modules` branch. The guidelines recommend organizing new files according to the existing repository structure. However, the link to the field-specific guidance appears to be broken. Looking at the repository, I see that

data/genomics/eukaryotes/

contains organism-specific directories, generally named using the scientific name (e.g.

arabidopsis_thaliana

,

saccharomyces_cerevisiae

and

gallus_gallus

). My module works with C. elegans gene identifiers and requires several types of input data: 1. Gene lists (CSV): A simple CSV containing WormBase IDs (e.g.

WBGene00001386

) or Worm Sequence IDs. Additional columns, if present, are ignored. 2. Gene lists (Excel): An Excel workbook containing one or more worksheets, each with a list of WormBase IDs. 3. Background gene set (CSV): A list of genes representing the background population for enrichment analysis, such as all genes detected in an experiment. This is generally a superset of the genes in the input comparison list. 4. Gene annotation file (CSV): A reference file mapping WormBase IDs and sequence IDs to hierarchical functional categories. This is used for gene enrichment analysis. 5. DESeq2 results (CSV): Differential expression results containing columns such as

baseMean

,

log2FoldChange

,

pvalue

, and

padj

, used for additional downstream analysis. I have a couple questions: 1. Would the appropriate location for these files be a new

data/genomics/eukaryotes/caenorhabditis_elegans/

directory, following the existing organism-specific naming convention? 2. Within that directory, should files be organized by format (e.g.

csv/

,

xlsx/

) or grouped by their purpose? An example structure might look like the below data/ └── genomics/ └── eukaryotes/ └── caenorhabditis_elegans/ ├── csv/ ├── xlsx/ └── ... Thanks for any guidance!

directory name is fine, i would group it by purpose

Hi all, @mashehu I've submitted PR #2356 to the modules branch: "Add test dataset for wormcat". I've followed the guidance provided here for the directory structure and organization of the test data. As this is my first contribution to the repository, I just wanted to make sure I've covered everything required on my end. Please let me know if there's anything else I need to address. Thanks, Dan