Make the main 3 processes pipe-friendly to avoid intermediate outputs

IARCbioinfo / needlestack

Multi-sample somatic variant caller

GNU General Public License v3.0

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Make the main 3 processes pipe-friendly to avoid intermediate outputs #147

Closed mfoll closed 7 years ago

mfoll commented 7 years ago

We should have a single process like samtools mpileup | mpileup2table | needlestack.r Linked with #146 This involves important changes in needlestack.nf and needlestack.r.