Input file name collision #121
Description
Description of the bug
Hello,
I am running several samples using spatialvi in different directories and they are all throwing the same error. Hope you can help:
I run spatialvi as follows:
nextflow run nf-core/spatialvi -r dev -profile singularity --outdir ./ --input ./sample.sheet.csv --spaceranger_probeset path/to/probe/set/Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv
My sample sheet looks like this:
sample,fastq_dir,cytaimage,slide,area
sample name,path/to/fastq/dirs/sample name,path/to/img/dir/image name,slide ID,area
The error message is as follows:
ERROR ~ Error executing process > 'NFCORE_SPATIALVI:SPATIALVI:READ_DATA (1)'
Caused by:
Process NFCORE_SPATIALVI:SPATIALVI:READ_DATA input file name collision -- There are multiple input files for each of the following file names: sample name/scalefactors_json.json, sample name/raw_feature_bc_matrix.h5, sample name/tissue_hires_image.png, sample name/tissue_lowres_image.png
Container:
/path/to/running/dir/work/singularity/docker.io-erikfas-spatialvi.img
Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh
-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '.nextflow.log' file for details
Command used and terminal output
Relevant files
No response
System information
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