Ilya Shlyakhter

There are also de novo scaffolding tools I wanted to look at, that scaffold based on read pairs rather than a reference (as part of a general effort to make...

"changing these recipes to the exact way we prefer may take some efforts" -- what changes are needed? Is there a danger that they'll impact other packages negatively? In bioconda...

@tomkinsc @dpark01 from @yesimon "The problem with drops in coveralls coverage after updating a branch is because I made a change in the tests to only run unit versus integration...

@yesimon We needn't update the cache every time. If no state is stored for any tests, we store it for all the tests. We use stored state to skip tests,...

Btw, one can check whether the list of files relevant to a test was correctly determined: just erase all others, and re-run the test. (Or, more reasonably, link just the...

@dpark01 @tomkinsc I've pushed the Sealer changes to the branch is-add-sealer ( https://github.com/broadinstitute/viral-ngs/tree/is-add-sealer ). There are several changes I wanted to make before merging it, though, like adding timeouts to...

[readjoiner_bug.tar.gz](https://github.com/genometools/genometools/files/1943506/readjoiner_bug.tar.gz)

@gordon @ggonnella this happened when using readjoiner as part of https://github.com/chjiao/PEHaplo pipeline

The workflow that's causing the issue is for comparing the results of two NGS pipelines across a range of datasets and conditions. So filenames look like "results/{PROJECT}/{POOL}/{SUBSAMP}/{PIPECONF}/{PIPENAME}/some_file.tsv" representing results for...

Humans rarely need to "make sense" of whole long pathnames at once. They just follow one path component at a time. I've had no trouble with the pretty straightforward data...