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nmdp-bioinformatics / pipeline

Consensus assembly and allele interpretation pipeline.
GNU Lesser General Public License v3.0
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write wrapper script for groovy. #17

Closed janders3-nmdp closed 9 years ago

janders3-nmdp commented 9 years ago

ensure it can find the workdir, and get all the ngs-tools jars. Note that this can't proceed until we have ngs-tools available.

ghost commented 9 years ago

Please don't do this. I won't be merging #14 and am leaning towards -1 it.

janders3-nmdp commented 9 years ago

sorry, wasn't trying to step on toes. I was just trying to set it up so people wouldn't have to type a 90 bazillion character command at the hackathon.

ghost commented 9 years ago

It should just be a command from ngs-tools, something like

$ filter-consensus -i input.bam -x genome.txt -o filtered.fasta -g HLA-A -m -c -b 0.5
ghost commented 9 years ago

Closing this issue in favor of #39.