Problem when defining SRA accession instead of fq1/fq2 hardfiles

[plycrsk]

Hi,

Firstly, thanks so much for the workflow, it's mostly working fine.

However, I'm receiving the following error when providing SRA input instead of fq1/fq2 (hard-files):

InputFunctionException in line 1 of https://github.com/snakemake-workflows/rna-seq-star-deseq2/raw/v1.2.0/workflow/rules/align.smk:
Error:
KeyError: 'fq1'
Wildcards:
sample=SRR5344335
unit=lane1
Traceback:
File "https://github.com/snakemake-workflows/rna-seq-star-deseq2/raw/v1.2.0/workflow/rules/common.smk", line 109, in get_fq

This seems to correspond to the following code:

u = units.loc[(wildcards.sample, wildcards.unit), ["fq1", "fq2"]].dropna()
if pd.isna(u["fq1"]):

where the first line is dropping the columns fq1/fq2 as they are empty, and line 2 is then false, so the accession is not defined/throws an error.

Here are the two input files. Working fine with fq1/fq1 input, but not with SRR input.

Thanks!
Sam