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Error with CONCAT_H5AD #330
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Thanks for reporting! Could you please paste the entire |
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``` |
It seems like when the function read_samplesheet reads the samplesheet, it takes the values in the column expected_cells as int, and the join method expects a str.
|
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
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