Help with running test command

[Chrisdoan9]

Hi team,

I try to use this nice pipeline but got error. Would you please have a look? Thank you so much!
nextflow run nf-core/spatialvi -profile singularity,test -r dev

Command used and terminal output

executor >  local (6)
[b7/bf6809] process > NFCORE_SPATIALVI:SPATIALVI:INPUT_CHECK:UNTAR_SPACERANGER_INPUT (fastq_dir.tar.gz)                        [100%] 1 of 1 ✔
[-        ] process > NFCORE_SPATIALVI:SPATIALVI:INPUT_CHECK:UNTAR_DOWNSTREAM_INPUT                                            -
[05/fd273b] process > NFCORE_SPATIALVI:SPATIALVI:FASTQC (CytAssist_11mm_FFPE_Human_Glioblastoma_2)                             [100%] 1 of 1 ✔
[9d/6e20e8] process > NFCORE_SPATIALVI:SPATIALVI:SPACERANGER:SPACERANGER_UNTAR_REFERENCE (homo_sapiens_chr22_reference.tar.gz) [100%] 1 of 1 ✔
[c1/d58a6c] process > NFCORE_SPATIALVI:SPATIALVI:SPACERANGER:SPACERANGER_COUNT (CytAssist_11mm_FFPE_Human_Glioblastoma_2)      [100%] 1 of 1 ✔
[67/a38a6e] process > NFCORE_SPATIALVI:SPATIALVI:READ_DATA (CytAssist_11mm_FFPE_Human_Glioblastoma_2)                          [100%] 1 of 1 ✔
[e6/f87d4d] process > NFCORE_SPATIALVI:SPATIALVI:DOWNSTREAM:QUALITY_CONTROLS (CytAssist_11mm_FFPE_Human_Glioblastoma_2)        [  0%] 0 of 1
[-        ] process > NFCORE_SPATIALVI:SPATIALVI:DOWNSTREAM:CLUSTERING                                                         -
[-        ] process > NFCORE_SPATIALVI:SPATIALVI:DOWNSTREAM:SPATIALLY_VARIABLE_GENES                                           -
[-        ] process > NFCORE_SPATIALVI:SPATIALVI:MULTIQC        
ERROR ~ Error executing process > 'NFCORE_SPATIALVI:SPATIALVI:DOWNSTREAM:QUALITY_CONTROLS (CytAssist_11mm_FFPE_Human_Glioblastoma_2)'
Caused by:
  Process `NFCORE_SPATIALVI:SPATIALVI:DOWNSTREAM:QUALITY_CONTROLS (CytAssist_11mm_FFPE_Human_Glioblastoma_2)` terminated with an error exit status (1)

Relevant files

nextflow.log

System information

nextflow/24.04.4

[fasterius]

Looking at your logfile, it that this is very similar to an issue mentioned on Slack before: https://nfcore.slack.com/archives/C031QFFTT7G/p1730398090267079. Could you go through the steps outlined there and see if that solves the issue for you?

[fasterius]

Closing this issue as per discussions in Slack (https://nfcore.slack.com/archives/C031QFFTT7G/p1733842053737099).