vcf_collect fusion split error

[berguner]

Description of the bug

Hi,
For some samples the pipeline (version 3.0.1) fails giving the error below:

Caused by:
  Essential container in task exited

Command executed:

  vcf_collect.py --fusioninspector RNA2956_3.FusionInspector.fusions.abridged.tsv.annotated.coding_effect --fusionreport RNA2956_3_fusionreport_index.html --fusioninspector
_gtf RNA2956_3.tsv --fusionreport_csv RNA2956_3.fusions.csv --hgnc hgnc_complete_set.txt --sample RNA2956_3 --out RNA2956_3_fusion_data.vcf
  gzip RNA2956_3_fusion_data.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT":
      python: $(python --version | sed 's/Python //g')
      HGNC DB retrieval: $(cat HGNC-DB-timestamp.txt)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "//nextflow-bin/vcf_collect.py", line 505, in <module>
      sys.exit(main())
               ^^^^^^
    File "//nextflow-bin/vcf_collect.py", line 493, in main
      vcf_collect(
    File "//nextflow-bin/vcf_collect.py", line 42, in vcf_collect
      .join(read_build_fusionreport(fusionreport_in_file), how="outer", on="FUSION")
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "//nextflow-bin/vcf_collect.py", line 340, in read_build_fusionreport
      fusion_report[["GeneA", "GeneB"]] = fusion_report["FUSION"].str.split("--", expand=True)
      ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^
    File "/usr/local/lib/python3.11/site-packages/pandas/core/frame.py", line 3966, in __setitem__
      self._setitem_array(key, value)
    File "/usr/local/lib/python3.11/site-packages/pandas/core/frame.py", line 4008, in _setitem_array
      check_key_length(self.columns, key, value)
    File "/usr/local/lib/python3.11/site-packages/pandas/core/indexers/utils.py", line 401, in check_key_length
      raise ValueError("Columns must be same length as key")
  ValueError: Columns must be same length as key

It sounds like one of the input files contains fusion gene pairs that would give more/less than 2 genes when split with --. I checked the fusions.csv and .fusionreport.tsv files but that wasn't the case. I am baffled why this error is occurring.

I am also attaching the nextflow.log file
vcf_collect_error.nextflow.log

Command used and terminal output

No response

Relevant files

No response

System information

No response

[rannick]

I just merged a few fixes for vcf_collect in dev, could you try with that branch and report the behaviour please?

[berguner]

I tried the dev branch but I got a different error now:

Command executed:

  vcf_collect.py --fusioninspector RNA2600_5.FusionInspector.fusions.abridged.tsv.annotated.coding_effect --fusionreport RNA2600_5_fusionreport_index.html --fusioninspector_gtf RNA2600_5.tsv --fusionreport_csv RNA2600_5.fusions.csv --hgnc hgnc_complete_set.txt --sample RNA2600_5 --out RNA2600_5_fusion_data.vcf
  gzip RNA2600_5_fusion_data.vcf
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:VCF_COLLECT":
      python: $(python --version | sed 's/Python //g')
      HGNC DB retrieval: $(cat HGNC-DB-timestamp.txt)
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Traceback (most recent call last):
    File "//nextflow-bin/vcf_collect.py", line 528, in <module>
      sys.exit(main())
               ^^^^^^
    File "//nextflow-bin/vcf_collect.py", line 516, in main
      vcf_collect(
    File "//nextflow-bin/vcf_collect.py", line 42, in vcf_collect
      .join(read_build_fusionreport(fusionreport_in_file), how="outer", on="FUSION")
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "//nextflow-bin/vcf_collect.py", line 339, in read_build_fusionreport
      fusion_report = pd.DataFrame.from_dict({k: [v] for k, v in expression.items()})
                                                                 ^^^^^^^^^^^^^^^^
  AttributeError: 'tuple' object has no attribute 'items'

[rannick]

This should be solved by #481