Snakemake bug when contig header contains FASTA file name

[CarraraAlessia]

Hi,

I noticed that the pipeline fails at rule 'compress_contig_fastqs' if the filename of my FASTA file is contained in the contig header.
E.g. sample1.fna & >sample1_contig1

Thanks for fixing it or mentioning it in the documentation!

Cheers! :)))

[farchaab]

Hello Alessia !

Can you provide an example fasta and input table to reproduce your error ?

[CarraraAlessia]

Hi,
Here are the command and input files to reproduce the error:

mess simulate -i simulate_test.csv --fasta fasta/

simulate_test.csv
NC.fna.gz