InputFunctionException in line 29 .../quant.smk

[amitfenn]

The error message:

$ snakemake --cores 80 --use-conda --dry-run
Building DAG of jobs...
~/miniconda3/envs/snakeflow-kallisto-sleuth/lib/python3.9/site-packages/pandas/core/indexing.py:925: PerformanceWarning: indexing past lexsort depth may impact performance.
  return self._getitem_tuple(key)
InputFunctionException in line 29 of https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/raw/v2.3.0/workflow/rules/quant.smk:
Error:
  ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().
Wildcards:
  sample=20SE01776
  unit=1
Traceback:
  File "https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/raw/v2.3.0/workflow/rules/common.smk", line 77, in get_trimmed
  File "~/miniconda3/envs/snakeflow-kallisto-sleuth/lib/python3.9/site-packages/pandas/core/generic.py", line 1537, in __nonzero__

My config files:

$ head config/*tsv
==> config/samples.tsv <==
sample  condition       batch_effect
20SE01776       1       London
20SF01123       1       London
20SH01318       1       London
20SH01483       1       London
20SI01410       1       London
20SP01339       1       London
20SS01190       1       London
20ST01399       1       London
20SW01296       1       London

==> config/units.tsv <==
sample  unit    fragment_len_mean       fragment_len_sd fq1     fq2
20SE01776       1       NA      NA      .../20SE01776_unmapped_left.fq .../20SE01776_unmapped_right.fq
20SF01123       1       NA      NA      .../20SF01123_unmapped_left.fq .../20SF01123_unmapped_right.fq 
(absolute paths given)

Thank you for this module in reproducible science. I really appreciate Snakemake and it's workflows.
However, this is my first attempt could you help me get this workflow running? The documentation is a bit scarce.

[dlaehnemann]

Sorry, we somehow missed this issue.

The part of the config that you posted looks OK. But as you mention that the docs are not that great: I have recently reworked the documentation for setting up your own instance of the workflow, but this is not yet released and thus not yet displayed in the snakemake workflow catalog. Maybe this already helps:
https://github.com/snakemake-workflows/rna-seq-kallisto-sleuth/tree/ecc9ab712b94e175a2c9e7c79b365faa98a3df44/config

Otherwise, it might make sense to switch to the newest release of the workflow, which is v2.5.1 (you are using v2.3.0. We constantly fix things, so the underlying cause might already have been fixed.

And finally, the error about the truth value of a Series might indicate that you are getting a Series (basically a pandas list of things) instead of a single item somewhere, so maybe you have some sort of duplicate in your units.tsv (or samples.tsv) somewhere beyond the head part.

If none of these help, maybe posting the full configuration can get us closer to a solution.