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• nf-core modules documentation

Description of the bug

Test [949573c5] 'decoupler_test'
> N E X T F L O W ~ version 24.04.4
> Launching /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/meta/mock.nf [prickly_leavitt] DSL2 - revision: 6a2b47e621
> Creating env using conda: conda-forge::decoupler-py=1.6.0 [cache /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2]
> [63/ce7666] Submitted process > DECOUPLER (test)
> ERROR ~ Error executing process > 'DECOUPLER (test)'
>
> Caused by:
> Process DECOUPLER (test) terminated with an error exit status (1)
>
>
> Command executed:
>
> #!/usr/bin/env python3
> import os
> import pandas as pd
>
> os.environ["NUMBA_CACHE_DIR"] = "./tmp"
>
> import decoupler as dc
>
> methods = ['aucell', 'gsea', 'gsva', 'mdt', 'mlm', 'ora', 'udt',
> 'ulm', 'viper', 'wmean', 'wsum']
>
> mat = pd.read_csv("expression.tsv", sep=" ", index_col=0)
> net = pd.read_csv("network.tsv", sep=" ", index_col=0)
>
> # Parsing arguments
> args = {'min_n': 1}
> parsedargs = {'args': {}}
>
> for k, v in args.items():
> # Specific method argument
> if k.split('')[0] in methods:
> meth = k.split('')[0]
> arg = ''.join(k.split('')[1:])
>
> if meth not in args['args'].keys():
> parsedargs['args'][meth] = {arg: v}
> else:
> parsedargs['args'][meth].update({arg: v})
>
> # Generic argument
> else:
> parsedargs[k] = v
>
>
> results = dc.decouple(
> mat=mat,
> net=net,
> - Of which 2 did not match due to:
> Overload in function 'np_arange': File: numba/np/arrayobj.py: Line 4760.
> With argument(s): '(start=int64, stop=int64, step=int64, dtype=class(float32))':
> Rejected as the implementation raised a specific error:
> TypingError: got some positional-only arguments passed as keyword arguments: 'start'
> raised from /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/numba/core/typing/templates.py:783
>
> During: resolving callee type: Function()
> During: typing of call at /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/decoupler/method_gsva.py (86)
>
>
> File "../../conda/env-e8572468eaade6843c07829a0101aaf2/lib/python3.12/site-packages/decoupler/method_gsva.py", line 86:
> def nb_get_D_I(mat):
>
> n = mat.shape[1]
> rev_idx = np.abs(np.arange(start=n, stop=0, step=-1, dtype=nb.f4) - n / 2)
> ^
>
> Work dir:
> /home/ubuntu/tests/949573c551759dbba21b380d94c814b5/work/63/ce7666b5e282eae692d5bdab4f1143
>
> Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
>
> -- Check '/home/ubuntu/tests/949573c551759dbba21b380d94c814b5/meta/nextflow.log' file for details
> WARN: Got an interrupted exception while taking agent result | java.lang.InterruptedException
Assertion failed:

assert process.success
| |
| false
DECOUPLER

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Relevant files

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System information

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