Fix ValueError

[alienzj]

>>> if pd.isna(u["fq1"]):
...     print("hello")
... 
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jiezhu/.conda/envs/bioenv/lib/python3.9/site-packages/pandas/core/generic.py", line 1537, in __nonzero__
    raise ValueError(
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().|

>>> if not pd.isna(u["fq1"]).all():
...     print("hello")
... 
hello

[alienzj]

➤ snakemake --cores all --dry-run -p -r -n
Workflow defines that rule get_genome is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule get_annotation is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule genome_faidx is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule bwa_index is eligible for caching between workflows (use the --cache argument to enable this).
Workflow defines that rule star_index is eligible for caching between workflows (use the --cache argument to enable this).
Building DAG of jobs...
File path 'sample_name  unit_name
VA003-M1B    L03          /lustre1/g/sph_tunlab/jiezhu/projects/c9_vacci...
Name: fq1, dtype: object' contains line break. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path 'sample_name  unit_name
VA003-M1B    L03          /lustre1/g/sph_tunlab/jiezhu/projects/c9_vacci...
Name: fq2, dtype: object' contains line break. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
MissingInputException in line 1 of /lustre1/g/sph_tunlab/jiezhu/projects/c9_vaccine_multi_omics/RNA_seq_analysis/assay/rna-seq-star-deseq2/workflow/rules/align.smk:
Missing input files for rule align:
sample_name  unit_name
VA003-M1B    L03          /lustre1/g/sph_tunlab/jiezhu/projects/c9_vacci...
Name: fq2, dtype: object
sample_name  unit_name
VA003-M1B    L03          /lustre1/g/sph_tunlab/jiezhu/projects/c9_vacci...
Name: fq1, dtype: object

[alienzj]

This PR is very useful when trimming is not performed.

[alienzj]

@johanneskoester Hi, Johannes, can you add me to the snakemake-workflows team ? I am happy to process some issues.

[dlaehnemann]

A lot has changed in the workflow, also affecting the code changes suggested here. And we now test for both a workflow run with trimming and one without. So I think this is fixed and tested now. But please open a new pull request if this persists or something else comes up.