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akcorut / kGWASflow

kGWASflow is a Snakemake workflow for performing k-mers-based GWAS.
https://github.com/akcorut/kGWASflow/wiki
MIT License
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The truth value of a Series is ambiguous #20

Closed pmoizerv closed 5 months ago

pmoizerv commented 11 months ago

I get the following error while trying to run using the command (trying to run with no sra, providing fq1 and fq2):
kgwasflow run -t 11 -c config/config.yaml -n --debug-dag 

Building DAG of jobs...
candidate job all
    wildcards: 
candidate job multiqc
    wildcards: 
InputFunctionException in rule fastqc in file /home/panazerv/.conda/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/qc.smk, line 5:
Error:
  ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
Wildcards:
  sample=L92-diploid_S22
  library=UC-2912
Traceback:
  File "/home/panazerv/.conda/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/common.smk", line 166, in get_individual_fastq
  File "/home/panazerv/.conda/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/common.smk", line 154, in is_sra_se
  File "/home/panazerv/.conda/envs/kgwasflow/lib/python3.11/site-packages/workflow/rules/common.smk", line 150, in sra_only
  File "/home/panazerv/.conda/envs/kgwasflow/lib/python3.11/site-packages/pandas/core/generic.py", line 1527, in __nonzero__

Any ideas on what is going wrong?

akcorut commented 11 months ago

Hi @pmoizerv,

It seems to me that the problem is probably caused by the samples.tsv file. Would it be possible for you to share that file with me?

akcorut commented 5 months ago

Closing this issue due to the lack of activity. Feel free to reopen if this issue persists.