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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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Question for the man #42

Closed mariogiov closed 9 years ago

mariogiov commented 9 years ago

Hey if I'm copying files over to a node to do variant calling and I've already done alignment, what do I actually need to copy? I'm thinking I'll copy the relevant 01_raw_alignment files for the sample in question but I don't expect I would need the 02_preliminary_alignment_qc files. Or? Do they get used in report gen or something? Part 2 if I don't copy e.g. the 02_preliminary_alignment_qc files how can I keep Piper from recreating them? Can I just add a .done file in that dir?

Yours truly,

The M-Man

johandahlberg commented 9 years ago

The easiest is if you copy the entire pipeline_output to the node. The 02_preliminary_alignment_qc is not that big, so I wouldn't expect copying that to the node will actually be a bottleneck.

mariogiov commented 9 years ago

Kk thanks