A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

Hello! I would like to add a small test set to `nf-core/test-datasets`... Could I get some advice?

For context - I want to add <https://github.com/nf-core/modules/pull/11306|this module> to filter adapters from pacbio HiFi data. I tried with all available pacbio data in `test-datasets` and none of those had adapters, so I made a small fastq myself to make the tests in this module meaningful... My dataset is a small fastq from the chicken gut microbiome (irrelevant for the sake of the test but maybe for the structure to follow in  `test-datasets`?) - what is the best place for it?

But I had to filter some reads - the original file was 20GBs

Then I think it's fine to add under a dedicated directory in `<https://github.com/nf-core/test-datasets/tree/modules/data/genomics/eukaryotes/>`

<https://github.com/nf-core/test-datasets/tree/modules/data/genomics/eukaryotes>

Oh I see, even if it's gut microbiome without host data?

Just need to describe in the main README  (or a dedicated README next to the file, where you describe exactly how you modified from the original data)

Gotcha, is it okay if I play around a bit and maybe post the PR in this thread when it's time to check it?

Thank you! Especially for replying while on holiday :grin:

Hi! I prepared a PR for my fastq file here: <https://github.com/nf-core/test-datasets/pull/2044>

Could I suggest to add a line to the instructions <https://github.com/nf-core/test-datasets/blob/modules/docs/ADD_NEW_DATA.md|here>? I struggled cloning the whole `test-datasets` repository - not sure if the issue was indexing the individual files or the history, but `git clone [url-to-fork]` was giving me:
```Cloning into 'test-datasets'...
remote: Enumerating objects: 37396, done.
remote: Counting objects: 100% (307/307), done.
remote: Compressing objects: 100% (208/208), done.
remote: Total 37396 (delta 187), reused 99 (delta 99), pack-reused 37089 (from 2)
Receiving objects: 100% (37396/37396), 33.20 GiB | 43.14 MiB/s, done.
fatal: fetch-pack: invalid index-pack output```
I solved this by installing only the `modules` branch:
```git clone -b modules --single-branch [url-to-fork]```
Maybe this can help others too

Ahh sorry <@U04LD4GQJUV>! Iti s here: <https://github.com/nf-core/test-datasets#downloading-test-data>

I didn't even know those instructions existed on the one you had!

I totally missed that!! Better this way :smile:

I think I am sorted anyway, <@U05LNHCFLCW> helped me with this over the weekend :slightly_smiling_face:

No regrets..our turn for Greece next :stuck_out_tongue: