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

nf-core

<@U08NXJ4HSCX> In the documentation regarding the medatata files for cellpainting
there is no files available at those links:
<s3://cellpainting-gallery/cpg0016-jump/source_4/workspace/metadata/external_metadata/>
<s3://cellpainting-gallery/cpg0016-jump/source_4/workspace/metadata/platemaps/2021_04_26_Batch1/>

Sorry, I forgot that project currently has those files structured elsewhere.  The platemap can be subset from <https://github.com/jump-cellpainting/datasets/blob/main/metadata/well.csv.gz>  (The external metadata is unnecessary)

```df = pd.read_csv('<https://github.com/jump-cellpainting/datasets/raw/refs/heads/main/metadata/well.csv.gz>')
df = df.loc[df['Metadata_Plate']=='BR00117035'].reset_index(drop=True)
df = df.rename(columns={'Metadata_Plate':'plate_map_name','Metadata_Well':'well_position'})
df.to_csv('BR00117035.txt',sep='\t',index=False)```

The other file you need (barcode_platemap) can be made with
```df = pd.DataFrame(columns=['Assay_Plate_Barcode','Plate_Map_Name'])
df['Assay_Plate_Barcode'] = ['BR00117035']
df['Plate_Map_Name'] = ['BR00117035']
df.to_csv('barcode_platemap.csv',index=False)```