Only add genomes to final RKI FASTA and report.csv that meet QC criteria about porecov

[hoelzer]

Should be fine for now, but might be subject to changes over the next days/weeks :)

Maybe you can write to the summary rki folder:

• genomes_valid.fasta
• genomes_invalid.fasta
• rki_valid_report.csv (that only contains then the IDs of the valid genomes?)

By that, it should be also clear to the user what he can expect in every file?

[hoelzer]

@replikation is there still an output multi FASTA file that has ALL sequences? Actually, we would need that as well for downstream processing. However, for other uses the direct split into valid and invalid is good so what I can also do is:

cat rki/valid/genomes_valid.fasta rki/invalid/genomes_invalid.fasta > all_fasta 

for my downstream tasks

[replikation]

• oh good point. forgot about that. are the rki criteria correct now via president? or can I take straight from the "valid" column?

[replikation]

need to extract the "valid" sequence name. i think this can also be done based on channels

[replikation]

good idea. yeah i think ill add that tomorrow or so

[replikation]

rki/
    valid/
        genomes_valid.fasta
        rki_valid_report.csv
    invalid/
        genomes_invalid.fasta
        rki_invalid_report.csv