I've been trying to run through the GALAXY.org mtDNA workflow demo, the first one, and cannot get past the SAM to BAM step. After filtering for unique reads, the SAM:BAM tool will not convert the SAM to BAM because the header is apparently gone. I tried the Reheader tool, but it errors because the source dataset is not a bam file.
I'm following the demo steps exactly as presented and using the blood PCR1 demo dataset. Is there a way around this?