Nextflow stdout:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (Sample_X)'

Caused by:
  Process `NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD (Sample_X)` terminated with an error exit status (1)


Command executed [/home/runner/work/scrnaseq/scrnaseq/./workflows/../subworkflows/local/../../modules/local/templates/mtx_to_h5ad_cellranger.py]:

  #!/usr/bin/env python
  
  # Set numba chache dir to current working directory (which is a writable mount also in containers)
  import os
  
  os.environ["NUMBA_CACHE_DIR"] = "."
  
  import scanpy as sc
  import pandas as pd
  import argparse
  from anndata import AnnData
  import platform
  
  def _mtx_to_adata(
      input: str,
      sample: str,
  ):
  
      adata = sc.read_10x_h5(input)
      adata.var["gene_symbols"] = adata.var_names
      adata.var.set_index("gene_ids", inplace=True)
      adata.obs["sample"] = sample
  
      # reorder columns for 10x mtx files
      adata.var = adata.var[["gene_symbols", "feature_types", "genome"]]
  
      return adata
  
  
  def format_yaml_like(data: dict, indent: int = 0) -> str:
      """Formats a dictionary to a YAML-like string.
      Args:
          data (dict): The dictionary to format.
          indent (int): The current indentation level.
      Returns:
          str: A string formatted as YAML.
      """
      yaml_str = ""
      for key, value in data.items():
          spaces = "  " * indent
          if isinstance(value, dict):
              yaml_str += f"{spaces}{key}:\n{format_yaml_like(value, indent + 1)}"
          else:
              yaml_str += f"{spaces}{key}: {value}\n"
      return yaml_str
  
  def dump_versions():
      versions = {
          "NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:MTX_TO_H5AD": {
              "python": platform.python_version(),
              "scanpy": sc.__version__,
              "pandas": pd.__version__
          }
      }
  
      with open("versions.yml", "w") as f:
          f.write(format_yaml_like(versions))
  
  def input_to_adata(
      input_data: str,
      output: str,
      sample: str,
  ):
      print(f"Reading in {input_data}")
  
      # open main data
      adata = _mtx_to_adata(input_data, sample)
  
      # standard format
      # index are gene IDs and symbols are a column
      adata.var['gene_versions'] = adata.var.index
      adata.var.index = adata.var['gene_versions'].str.split('.').str[0]
      adata.var_names_make_unique()
  
      # write results
      adata.write_h5ad(f"{output}", compression="gzip")
      print(f"Wrote h5ad file to {output}")
  
      # dump versions
      dump_versions()
  
      return adata
  
  #
  # Run main script
  #
  
  # create the directory with the sample name
  os.makedirs("Sample_X", exist_ok=True)
  
  # input_type comes from NF module
  adata = input_to_adata(
      input_data="filtered_feature_bc_matrix.h5",
      output="Sample_X/Sample_X_filtered_matrix.h5ad",
      sample="Sample_X"
  )

Command exit status:
  1

Command output:
  Reading in filtered_feature_bc_matrix.h5

Command error:
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  ba94160d36b7: Verifying Checksum
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  Digest: sha256:fbd40d3d00751ac0df11564b3697006ecf8604af48960833910d32755033575f
  Status: Downloaded newer image for community.wave.seqera.io/library/scanpy:1.10.2--e83da2205b92a538
  /opt/conda/lib/python3.12/site-packages/anndata/_core/anndata.py:1820: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
    utils.warn_names_duplicates("var")
  /opt/conda/lib/python3.12/site-packages/anndata/_core/anndata.py:1820: UserWarning: Variable names are not unique. To make them unique, call `.var_names_make_unique`.
    utils.warn_names_duplicates("var")
  Reading in filtered_feature_bc_matrix.h5
  Traceback (most recent call last):
    File ".command.sh", line 92, in <module>
      adata = input_to_adata(
              ^^^^^^^^^^^^^^^
    File ".command.sh", line 76, in input_to_adata
      adata.write_h5ad(f"{output}", compression="gzip")
    File "/opt/conda/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1929, in write_h5ad
      write_h5ad(
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 105, in write_h5ad
      write_elem(f, "var", adata.var, dataset_kwargs=dataset_kwargs)
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 359, in write_elem
      Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/utils.py", line 243, in func_wrapper
      return func(*args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 309, in write_elem
      return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 57, in wrapper
      result = func(g, k, *args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 691, in write_dataframe
      raise ValueError(
  ValueError: DataFrame.index.name ('gene_versions') is also used by a column whose values are different. This is not supported. Please make sure the values are the same, or use a different name.
  Error raised while writing key 'var' of <class 'h5py._hl.group.Group'> to /

Work dir:
  /home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/17493f5b507e3df5263c89c8572a97f1/work/8f/a867bef0daf7245c50216b049bdd70

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

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/17493f5b507e3df5263c89c8572a97f1/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '/home/runner/work/scrnaseq/scrnaseq/.nf-test/tests/17493f5b507e3df5263c89c8572a97f1/meta/nextflow.log' file for details
Nextflow stderr:

Nextflow 24.10.0 is available - Please consider updating your version to it