Mismatch of the output paths in snapshot file #109
Description
Description of the bug
Attached below is the screenshot of the snap file
image based mode should have output paths prefixed with image and not coordinate
{
"-profile test": {
"content": [
{
"UNTAR": {
"untar": 1.34
},
"Workflow": {
"nf-core/spatialxe": "v1.0dev"
}
},
[
"coordinate",
"coordinate/xeniumranger",
"coordinate/xeniumranger/import_segementation",
"coordinate/xeniumranger/import_segementation/test_run",
"coordinate/xeniumranger/import_segementation/test_run/outs",
"coordinate/xeniumranger/import_segementation/test_run/outs/fake_file.txt",
"coordinate/xeniumranger/import_segementation/versions.yml",
"image",
"image/baysor",
"image/baysor/run",
"image/baysor/run/test_run",
"image/baysor/run/test_run/segmentation.csv",
"image/baysor/run/test_run/segmentation_polygons_2d.json",
"image/baysor/run/versions.yml",
"image/cellpose_cells",
"image/cellpose_cells/test_run",
"image/cellpose_cells/test_run/morphology.ome_cells_masks.tif",
"image/cellpose_cells/test_run/morphology.ome_cells_seg.npy",
"image/cellpose_cells/versions.yml",
"image/multiqc",
"image/multiqc/raw_bundle",
"image/multiqc/raw_bundle/multiqc_data",
"image/multiqc/raw_bundle/multiqc_plots",
"image/multiqc/raw_bundle/multiqc_report.html",
"image/multiqc/redefined_bundle",
"image/multiqc/redefined_bundle/multiqc_data",
"image/multiqc/redefined_bundle/multiqc_plots",
"image/multiqc/redefined_bundle/multiqc_report.html",
"image/spatialdata",
"image/spatialdata/merge",
"image/spatialdata/merge/spatialdata",
"image/spatialdata/merge/spatialdata/test_run",
"image/spatialdata/merge/spatialdata/test_run/merged_bundle",
"image/spatialdata/merge/spatialdata/test_run/merged_bundle/fake_file.txt",
"image/spatialdata/merge/versions.yml",
"image/spatialdata/meta",
"image/spatialdata/meta/spatialdata",
"image/spatialdata/meta/spatialdata/test_run",
"image/spatialdata/meta/spatialdata/test_run/metadata",
"image/spatialdata/meta/spatialdata/test_run/metadata/fake_file.txt",
"image/spatialdata/meta/versions.yml",
"image/spatialdata/write",
"image/spatialdata/write/spatialdata",
"image/spatialdata/write/spatialdata/test_run",
"image/spatialdata/write/spatialdata/test_run/raw_bundle",
"image/spatialdata/write/spatialdata/test_run/raw_bundle/fake_file.txt",
"image/spatialdata/write/spatialdata/test_run/redefined_bundle",
"image/spatialdata/write/spatialdata/test_run/redefined_bundle/fake_file.txt",
"image/spatialdata/write/versions.yml",
"image/untar",
"image/untar/test_run",
"image/untar/test_run/experiment.xenium",
"image/untar/test_run/gene_panel.json",
"image/untar/test_run/morphology.ome.tif",
"image/untar/test_run/transcripts.parquet",
"image/untar/versions.yml",
"image/utility",
"image/utility/resize_tif",
"image/utility/resize_tif/test_run",
"image/utility/resize_tif/test_run/resized_morphology.ome_cells_masks.tif.tif",
"image/utility/resize_tif/versions.yml",
"pipeline_info",
"pipeline_info/nf_core_spatialxe_software_mqc_versions.yml"
],
[
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,124884bd49548c3ea63ddf29d238c589",
"segmentation.csv:md5,d41d8cd98f00b204e9800998ecf8427e",
"segmentation_polygons_2d.json:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,a072fc212a30ce4d87379d0871eff5fb",
"morphology.ome_cells_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
"morphology.ome_cells_seg.npy:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,98fed7928a2da3470a39e1f74022a899",
"multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
"multiqc_report.html:md5,d41d8cd98f00b204e9800998ecf8427e",
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,9010b5ed380b88a5b20ca6dae73345cb",
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,1dfc19eaa8a0746f17aad700d797e323",
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,5ffb7137a403934431ca87be7ad84968",
"experiment.xenium:md5,d41d8cd98f00b204e9800998ecf8427e",
"gene_panel.json:md5,d41d8cd98f00b204e9800998ecf8427e",
"morphology.ome.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
"transcripts.parquet:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,4054f048e726d8faf84c982f8180a9e0",
"resized_morphology.ome_cells_masks.tif.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
"versions.yml:md5,686bf4196185d2e13ae2e12221233b7e"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-10-29T13:22:11.312536"
}
}
Command used and terminal output
Relevant files
No response
System information
No response