We tried to run this nf-core/spatialaxe on a publicly available Xenium dataset using Seqera Tower and AWS batch. It seems to run into the following file check error when running on AWS batch with fusion. What could be causing this issue? This has happened with and without

Missing required file(s) in xenium bundle '<s3://xxxx/data/spatial_transcriptomics/xenium/public/mouse/GSE272303-SNCA-tg/Line61nTg_1/outs>': [cell_boundaries.csv.gz, cell_boundaries.parquet, cell_feature_matrix.h5, cell_feature_matrix.zarr.zip, cells.csv.gz, cells.parquet, cells.zarr.zip, experiment.xenium, gene_panel.json, metrics_summary.csv, morphology.ome.tif, morphology_focus/, nucleus_boundaries.csv.gz, nucleus_boundaries.parquet, transcripts.parquet, transcripts.zarr.zip]

Hi Kokul. Can you see what files are available in the task work directory? Are any of the staged inputs symlinks to files located elsewhere?

Hey Rob, there are no symlinks for this pipeline. The pipeline author @Florian Heyl it taking a look at this issue on another thread.

Ok, no worries. I'll let Florian run with it for a bit, but feel free to ping me if you run into any issues.