ANNDATA_BARCODES terminates with Missing output file(s) *.h5ad expected by process

[fbnrst]

Description of the bug

I started a run of the dev branch and I did run into the following error:

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES (Fibrosis-LT_Agg20_Second)'

Caused by:
  Missing output file(s) `*.h5ad` expected by process `NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES (Fibrosis-LT_Agg20_Second)` (note: input files are not included in the default matching set)


Command executed [/home/rost/.nextflow/assets/nf-core/scrnaseq/./workflows/../subworkflows/nf-core/h5ad_removebackground_barcodes_cellbender_anndata/../../../modules/nf-core/anndata/barcodes/templates/barcodes.py]:

  #!/usr/bin/env python3

  import platform

  import anndata as ad
  import pandas as pd


  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


  df = pd.read_csv("Fibrosis-LT_Agg20_Second_cell_barcodes.csv", header=None)
  adata = ad.read_h5ad("Fibrosis-LT_Agg20_Second_raw_matrix.h5ad")

  adata = adata[df[0].values]

  adata.write_h5ad("Fibrosis-LT_Agg20_Second_raw_matrix.h5ad")

  # Versions

  versions = {
      "NFCORE_SCRNASEQ:SCRNASEQ:H5AD_REMOVEBACKGROUND_BARCODES_CELLBENDER_ANNDATA:ANNDATA_BARCODES": {"python": platform.python_version(), "anndata": ad.__version__, "pandas": pd.__version__}
  }

  with open("versions.yml", "w") as f:
      f.write(format_yaml_like(versions))

Command exit status:
  0

Command output:
  (empty)

Command error:
  INFO:    Could not find any nv files on this host!

Work dir:
  /lustre/projects/mouse_assembloid/data_analysis/rost/fr_ma_3/analysis/04_nf-core_scrnaseq/work/af/97961ba68a1b0eb5b4ca9aedafb86b

Container:
  /projects/Fabian_Rost/home_stuff/nxf_singularity_cachedir/community.wave.seqera.io-library-anndata-0.10.9--d13580e4b297da7c.img

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

 -- 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

Seems like input and output file are the same in the python script.

I could work around by adding this to my nextflow.config:

withName: ANNDATA_BARCODES {
        ext.prefix = 'output'
    }

Command used and terminal output

Relevant files

No response

System information

No response