BAM as expected ONT input

[SergejN]

Dear @mrvollger ,

sorry if I misunderstood, but from the code (https://github.com/mrvollger/SDA/blob/1fbe948f3d8cde6ae6b8c49b33f4220053755718/SDA.smk#L110), it looks like the rule minimap2 expects the Nanopore data to be in a BAM file, which is not necessarily the case. The simplest (although admittedly not necessarily the most reliable) would be to look at the extension and differentiate between *.fq/*.fastq, *.fq.gz/*.fastq.gz and bam/sam.
My nanopore reads are stored as *.fastq.gz, therefore, I had to remove samtools fasta ... to make the pipeline work.

thanks! Sergej

[mrvollger]

Thanks for pointing out these mistakes! I will make commits for this and you other comment this evening!