Bam files for manta no longer saved (but still channeled to strelka)

[arontommi]

RunManta changed so that bam and bai files are no longer added to publishDir (results/Manta)

[maxulysse]

Hi, thanks a lot for your PR.
I didn't notice earlier this issue earlier.
It was only links to the files that were copied, but still annoying when you want to keep a clean repository.

[arontommi]

Hi and thanks for accepting,
As i understand it, since the links where hard, the bam files were taking up space in the results dir. I might however be wrong

[maxulysse]

From what I understand from hard linking, it doesn't take extra space, it's just a pointer to the same memory.