ET.py check file existence

[thomasmanke]

ET.py should assert existence of files and exist more gracefully if missing.
Use case: multiqc_samtools_flagstat.txt is not produced by multiQC 1.23
Suggestion: replace rates with NaN if undetermined?

[adRn-s]

Maybe there was another issue here and BRB needs to reprocess the whole thing. I would be surprised if their samtools module doesn't write the text file somewhere and then parse it.

PS. Actually, I went through MultiQC's changelog and their only stated changes were not related to moving the file or anything... I know, it doesn't prove anything. The change could've been done and not written.... but still,

1.23

The samtools flagstat test that verifies some logic in the flagstat submodule of the samtools module;

1.22

Add violin multiple datasets & samtools flagstat percentage switch (MultiQC/MultiQC#2430)

[thomasmanke]

I was also surprised, but I had explicitly tried (outside of BRB) all multiQC from snapePipe3.0.0 env (1.19), snakePipe3.1.0 (1.23) and 1.25 (per module load). Only 1.23 did not produce the multiqc_samtools_flagstat.txt file.

[WardDeb]

cfr. maxplanck-ie/snakepipes#1074
Note that this doesn't fix the need for a more 'graceful exit', which'd make this whole thing more robust.