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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Error with CONCAT_H5AD #330

Open ashwinikumarkulkarni opened 1 month ago

ashwinikumarkulkarni commented 1 month ago

Description of the bug

nf-core/scrnaseq test using conda fails with the following error message. Fetched from '.nextflow.log'. Thanks!

Caused by: Process NFCORE_SCRNASEQ:SCRNASEQ:MTX_CONVERSION:CONCAT_H5AD (1) terminated with an error exit status (1)

Command used and terminal output

nextflow run nf-core/scrnaseq -r 2.6.0 -profile test,conda --outdir test_scrnaseq

Relevant files

No response

System information

NEXTFLOW version 23.10.1 build 5891 nf-core/scrnaseq v2.6.0-gc5a6445 Linux HPC BioConda

grst commented 1 month ago

Thanks for reporting! Could you please paste the entire .command.log from the work directory? The work directory of the failed process is usually shown as part of the error message.

ashwinikumarkulkarni commented 1 month ago

Here is the '.command.log' output:



Traceback (most recent call last):
  File "/home2/akulk1/.nextflow/assets/nf-core/scrnaseq/bin/concat_h5ad.py", line 40, in <module>
    df_samplesheet = read_samplesheet(args["input"])
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home2/akulk1/.nextflow/assets/nf-core/scrnaseq/bin/concat_h5ad.py", line 20, in read_samplesheet
    df = df.groupby(["sample"]).agg(lambda column: ",".join(set(column)))
         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 1482, in aggregate
    result = gba.agg()
             ^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/apply.py", line 193, in agg
    return self.agg_list_like()
           ^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/apply.py", line 326, in agg_list_like
    return self.agg_or_apply_list_like(op_name="agg")
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/apply.py", line 1571, in agg_or_apply_list_like
    keys, results = self.compute_list_like(op_name, selected_obj, kwargs)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/apply.py", line 385, in compute_list_like
    new_res = getattr(colg, op_name)(func, *args, **kwargs)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 257, in aggregate
    ret = self._aggregate_multiple_funcs(func, *args, **kwargs)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 362, in _aggregate_multiple_funcs
    results[key] = self.aggregate(func, *args, **kwargs)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 294, in aggregate
    return self._python_agg_general(func, *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 327, in _python_agg_general
    result = self._grouper.agg_series(obj, f)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/ops.py", line 864, in agg_series
    result = self._aggregate_series_pure_python(obj, func)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/ops.py", line 885, in _aggregate_series_pure_python
    res = func(group)
          ^^^^^^^^^^^
  File "/project/Neuroinformatics_Core/Konopka_lab/akulk1/RESOURCES/BIOCONDA_NEXTFLOW/work/conda/env-8ceee76ce5640a76fa8925a8ce8f49a3/lib/python3.12/site-packages/pandas/core/groupby/generic.py", line 324, in <lambda>
    f = lambda x: func(x, *args, **kwargs)
                  ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home2/akulk1/.nextflow/assets/nf-core/scrnaseq/bin/concat_h5ad.py", line 20, in <lambda>
    df = df.groupby(["sample"]).agg(lambda column: ",".join(set(column)))
                                                   ^^^^^^^^^^^^^^^^^^^^^
TypeError: sequence item 0: expected str instance, int found```