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

nf-core

<@U08PG5879PD> <@U08V3KATH2M> <@U08NXFXNHD5> I've got a draft PR <https://github.com/nf-core/cellpainting/pull/27|here> that is generating the load_data_csvs for a subset of images (grouped by plate, group, and channel) and then tries to load them into a cellprofiler illumination pipeline. It's given me a image not found error, but I'm not sure if that's because cellprofiler is breaking due to nextflow's use of symlinks or if I'm not writing the load_data_csv file correctly. Would one of you mind running my draft PR pipeline taking a look?

I switched to using the `--image-directory {}` argument which seems like it should help. But still running into issues with the header naming.

I pulled the details out of the task execution that's failing to make it easier to see what's going on.  <https://github.com/nf-core/cellpainting/pull/27#issuecomment-3050086888>

`load_data.csv`'s expect the format of `FileName_CHANNEL` and `PathName_CHANNEL` (as I think is probably appropriate for NextFlow) OR `URL_CHANNEL` (as we have standardized in the Cell Painting Gallery). `CHANNEL` can be any string.

(I have never actually passed `--image-directory {}` , I always use `PathName_CHANNEL` columns in the .csv)