MultiQC config not found

[marcus-tutert]

Description of the bug

Hi,

This is a great tool however I'm running into a hurdle on the final step - regarding the multiQC reporting step. It appears to not be finding the multiqc config file?

jovyan@rlmt278-scdownstream-0:~/osteomics/projects/scdownstream$ nextflow run  /home/jovyan/osteomics/projects/scdownstream/scdownstream/  --input /home/jovyan/osteomics/projects/scdownstream/scdownstream/sample_sheet.csv --outdir ./results -c /cache-juicefs/nextflow-workspace/test/work/marcus_config.config --preprocess_only TRUE --ambient_removal soupx -resume 

 N E X T F L O W   ~  version 24.04.4

Launching `/home/jovyan/osteomics/projects/scdownstream/scdownstream/main.nf` [happy_lichterman] DSL2 - revision: 456139e594


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/scdownstream 0.0.1dev
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Input/output options
  input          : /home/jovyan/osteomics/projects/scdownstream/scdownstream/sample_sheet.csv
  outdir         : ./results

Pipeline options
  preprocess_only: true
  ambient_removal: soupx

Core Nextflow options
  runName        : happy_lichterman
  containerEngine: docker
  launchDir      : /home/jovyan/osteomics/projects/scdownstream
  workDir        : /cache-juicefs/nextflow-workspace/work
  projectDir     : /home/jovyan/osteomics/projects/scdownstream/scdownstream
  userName       : jovyan
  profile        : standard
  configFiles    : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The nf-core framework
    https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
    https://github.com/nf-core/scdownstream/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

* --max_memory: 1200.GB
* --max_cpus: 14
* --max_time: 7.d


executor >  k8s (4)
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_READH5                                  -
[94/e0d742] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READRDS (SAMN14430801)                   [100%] 2 of 2, cached: 2 ✔
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READCSV                                  -
[a5/e012e5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (SAMN14430801)                     [100%] 4 of 4, cached: 4 ✔
[2a/142145] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_UNFILTERED_SIZE (SAMN14430801)             [100%] 2 of 2, cached: 2 ✔
[-        ] NFC…SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND -
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:ADATA_BARCODES           -
[d4/39273a] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_FILTERED_SIZE (SAMN14430801)               [100%] 2 of 2, cached: 2 ✔
[56/8db6a1] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_RAW (SAMN14430801)                          [100%] 2 of 2, cached: 2 ✔
[32/6c1937] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:AMBIENT_RNA_REMOVAL:SOUPX (SAMN14430801)       [100%] 2 of 2, cached: 2 ✔
[a8/a6515b] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_FILTER (SAMN14430801)                   [100%] 2 of 2, cached: 2 ✔
[0b/799ebf] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_THRESHOLDED_SIZE (SAMN14430801)            [100%] 2 of 2, cached: 2 ✔
[8b/3178ae] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:SCANPY_SCRUBLET (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[fb/954257] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:DOUBLET_REMOVAL (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[ca/ef2870] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_DEDOUBLETED_SIZE (SAMN14430801)            [100%] 2 of 2, cached: 2 ✔
[3c/3b9bac] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_FILTERED (SAMN14430799)                     [100%] 2 of 2, cached: 2 ✔
[69/40a1d5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:COLLECT_SIZES (sizes)                          [100%] 1 of 1, cached: 1 ✔
[04/152249] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC                                                   [ 75%] 3 of 4, failed: 3, retries: 3
[79/eb0e4e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (1)
[ea/158996] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (2)
[77/661a8e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (3)
ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC'

Caused by:
  Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
executor >  k8s (4)
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_READH5                                  -
[94/e0d742] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READRDS (SAMN14430801)                   [100%] 2 of 2, cached: 2 ✔
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_READCSV                                  -
[a5/e012e5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (SAMN14430801)                     [100%] 4 of 4, cached: 4 ✔
[2a/142145] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_UNFILTERED_SIZE (SAMN14430801)             [100%] 2 of 2, cached: 2 ✔
[-        ] NFC…SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:CELLBENDER_REMOVEBACKGROUND -
[-        ] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:EMPTY_DROPLET_REMOVAL:ADATA_BARCODES           -
[d4/39273a] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_FILTERED_SIZE (SAMN14430801)               [100%] 2 of 2, cached: 2 ✔
[56/8db6a1] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_RAW (SAMN14430801)                          [100%] 2 of 2, cached: 2 ✔
[32/6c1937] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:AMBIENT_RNA_REMOVAL:SOUPX (SAMN14430801)       [100%] 2 of 2, cached: 2 ✔
[a8/a6515b] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:SCANPY_FILTER (SAMN14430801)                   [100%] 2 of 2, cached: 2 ✔
[0b/799ebf] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_THRESHOLDED_SIZE (SAMN14430801)            [100%] 2 of 2, cached: 2 ✔
[8b/3178ae] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:SCANPY_SCRUBLET (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[fb/954257] NFC…_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:DOUBLET_DETECTION:DOUBLET_REMOVAL (SAMN14430801) [100%] 2 of 2, cached: 2 ✔
[ca/ef2870] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:GET_DEDOUBLETED_SIZE (SAMN14430801)            [100%] 2 of 2, cached: 2 ✔
[3c/3b9bac] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:QC_FILTERED (SAMN14430799)                     [100%] 2 of 2, cached: 2 ✔
[69/40a1d5] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:COLLECT_SIZES (sizes)                          [100%] 1 of 1, cached: 1 ✔
[04/152249] NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC                                                   [100%] 4 of 4, failed: 4, retries: 3 ✘
[79/eb0e4e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (1)
[ea/158996] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (2)
[77/661a8e] NOTE: Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2) -- Execution is retried (3)
ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC'

Caused by:
  Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC` terminated with an error exit status (2)


Command executed:

  multiqc \
      --force \
       \
      --config multiqc_config.yml \
       \
       \
       \
       \
       \
      .
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:MULTIQC":
      multiqc: $( multiqc --version | sed -e "s/multiqc, version //g" )
  END_VERSIONS

Command exit status:
  2

Command output:
  (empty)

Command error:
                                                                                  
   /// MultiQC 🔍 v1.25.1                                                         
                                                                                  
   Usage: multiqc [OPTIONS] [ANALYSIS DIRECTORY]                                  
                                                                                  
   This is MultiQC v1.25.1                                                        
   For more help, run 'multiqc --help' or visit http://multiqc.info               
  ╭─ Error ──────────────────────────────────────────────────────────────────────╮
  │ Invalid value for '-c' / '--config': Path 'multiqc_config.yml' does not      │
  │ exist.                                                                       │
  ╰──────────────────────────────────────────────────────────────────────────────╯
                                                                                  

Work dir:
  /cache-juicefs/nextflow-workspace/work/04/152249a7d6ba23010d2d6e46c9d33a

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

 -- 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
-[nf-core/scdownstream] Pipeline completed with errors-

Command used and terminal output

No response

Relevant files

No response

System information

No response