nf-core
Input file name collision
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
No response
Hi,
Is your sample name actually "sample name" with a space? My guess is that the space is messing things up somehow. I can do some testing with spaces and see if I can reproduce. Could you test without the space in the sample name also?
No, sorry. The sample name has one of the two following formats: X00-000000_X0_X0X_0 or X00_000000_X0_X0X_0 where the Xs are different alphabetic characters and the 0s are different numeric characters.
Hi, I was not able to reproduce this locally unfortunately. Do you still have the issue @vella12-osu? If yes, could you share some examples with us so that we can replicate?