problem with the test case

[DavidSriker]

I try to use the tool with the test case but I got the following error (which refers to the 20191121_BRAC3438.6f.mcd)

>>> nextflow run nf-core/imcyto -profile test,docker
N E X T F L O W  ~  version 20.10.0
Launching `nf-core/imcyto` [marvelous_bhabha] - revision: b5877ce63f [master]
----------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/imcyto v1.0.0
----------------------------------------------------
Run Name                 : marvelous_bhabha
Input Files              : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/20191121_BRAC3438.6f.mcd
Metadata File            : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/inputs/metadata.csv
Full Stack cppipe File   : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/full_stack_preprocessing.cppipe
Ilastik Stack cppipe File: https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_stack_preprocessing.cppipe
Skip Ilastik Step        : No
Ilastik Training ilp File: https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/ilastik_training_params.ilp
Segmentation cppipe File : https://raw.githubusercontent.com/nf-core/test-datasets/imcyto/plugins/segmentation.cppipe
Max Resources            : 6 GB memory, 2 cpus, 12h time per job
Container                : docker - [:]
Output Dir               : ./results
Launch Dir               : /home/nucleai
Working Dir              : /home/nucleai/work
Script Dir               : /home/nucleai/.nextflow/assets/nf-core/imcyto
User                     : nucleai
Config Profile           : test,docker
Config Description       : Minimal test dataset to check pipeline function
----------------------------------------------------
executor >  local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [  0%] 0 of 1
executor >  local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[-        ] process > PREPROCESS_FULL_STACK           -
executor >  local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[-        ] process > PREPROCESS_FULL_STACK           -
executor >  local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[-        ] process > PREPROCESS_FULL_STACK           -
[-        ] process > PREPROCESS_ILASTIK_STACK        -
executor >  local (2)
[2e/3d5015] process > IMCTOOLS (20191121_BRAC3438.6f) [100%] 1 of 1, failed: 1 ✘
[-        ] process > PREPROCESS_FULL_STACK           -
[-        ] process > PREPROCESS_ILASTIK_STACK        -
[-        ] process > ILASTIK                         -
[-        ] process > SEGMENTATION                    -
[d4/a4bba6] process > output_documentation            [100%] 1 of 1 ✔
[-        ] process > get_software_versions           -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/imcyto] Pipeline completed with errors-
Error executing process > 'IMCTOOLS (20191121_BRAC3438.6f)'

Caused by:
  Process `IMCTOOLS (20191121_BRAC3438.6f)` terminated with an error exit status (1)

Command executed:

  run_imctools.py 20191121_BRAC3438.6f.mcd metadata.csv
  pip show imctools | grep "Version" > imctools_version.txt

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "/home/nucleai/.nextflow/assets/nf-core/imcyto/bin/run_imctools.py", line 73, in <module>
      parser = mcdparser.McdParser(args.INPUT_FILE)
    File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparser.py", line 31, in __init__
      McdParserBase.__init__(self, filename, filehandle, metafilename)
    File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparserbase.py", line 48, in __init__
      self.retrieve_mcd_xml()
    File "/usr/local/lib/python3.8/site-packages/imctools/io/mcdparser.py", line 73, in retrieve_mcd_xml
      raise ValueError('Invalid MCD: MCD xml start tag not found in file %s' % self.filename)
  ValueError: Invalid MCD: MCD xml start tag not found in file 20191121_BRAC3438.6f.mcd

Work dir:
  /home/nucleai/work/2e/3d50156173d45bbca8d5be8dae1dd3

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Can you please suggest a way of fixing it?
Thanks