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trinityrnaseq / trinityrnaseq

Trinity RNA-Seq de novo transcriptome assembly
BSD 3-Clause "New" or "Revised" License
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samples_idx in align_and_estimate_abundance.pl not in effect #1379

Open tomoakin opened 7 months ago

tomoakin commented 7 months ago

Since commit b78ff782c4e92a7a77a3598bfe1d0e859d31149b, samples_idx parameter apparently have no effect. Reverting this commit recover the expected behavior that a single sample out of many samples can be processed, allowing parallel computing over many nodes on a cluster. With current state, all the parallel process executes from index 1 and thus disrupting the file each other to make the abundance estimation process fail. The reason of removal here is not very clear to me; there might have been some necessity for debugging. I hope the function recovered or removed from the help to make them coherent with the documentation.

brianjohnhaas commented 7 months ago

restored under dev for now, but should be refactored or redone later so it's more intuitive.

brianjohnhaas commented 7 months ago

Leaving this open as a reminder to deal with this properly at some point.