Ilya Shlyakhter

from human depletion databases, mask any sequence similar to viral or bacterial

1

Reduce the chance of erroneously depleting viral or bacterial sequences that have remote homology to human.

Warnings can get lost in logging output; gather them and print them at the end, like GATK does. Maybe save them to an output file.

When using the system clock to choose a random seed, save the seed that was used, so the results can be reproduced.

speed up build by skipping tests unaffected by changed code

4

Could try one of https://pypi.python.org/pypi/pytest-testmon https://pypi.python.org/pypi/pytest-incremental https://pypi.python.org/pypi/pytest-cov-exclude https://pypi.python.org/pypi/pytest-cagoule https://pypi.python.org/pypi/pytest-knows https://pypi.python.org/pypi/pytest-skipper https://github.com/ChrisBeaumont/smother together with https://docs.travis-ci.com/user/caching/ Would need to pass cached coverage info for skipped tests to coveralls, so that skipped tests...

See https://github.com/broadinstitute/viral-ngs/pull/627#issuecomment-314559738 . Fix cluster submission scripts to properly handle included config files, which would enable the [easy-deploy script](https://github.com/broadinstitute/viral-ngs-deploy/tree/master/easy-deploy-script) to copy just a stub config file that would just reference...

readjoiner assertion failure

2

## Problem description readjoiner fails with an assertion: $ gt readjoiner overlap -readset samp -l 90 # gt readjoiner overlap (version 1.2) # number of reads in filtered readset =...

rule option to automatically shorten pathnames passed to commands

8

**Is your feature request related to a problem? Please describe.** Pathnames in Snakemake can get very long, and command lines even longer. This helps with data organization by explicitly encoding...

fixed file type in description of read_json()

7

### Checklist - [X] Pull request details were added to CHANGELOG.md

fix illustration of differences between inputs and intermediate values

1

### Checklist - [X] Pull request details were added to CHANGELOG.md

use localized filenames for File inputs used in expressions in Non-Input Declarations

2

Currently, the spec says: "When a WDL author uses a File input in their **Command Section**, the fully qualified, localized path to the file is substituted into the command string."...