Chris Tomkins-Tinch

Related to this, a [`ghostx`](https://anaconda.org/bioconda/ghostx) package has been added to bioconda so we can more easily include/evaluate it, as well as one for [`ghostz`](https://anaconda.org/bioconda/ghostz).

Have you set the `config.yaml` file to use a path containing a BLAST depletion database? We have a few pre-built databases described in section 4.2.3 of the docs: http://viral-ngs.readthedocs.io/en/latest/pipeuse.html#setting-up-an-analysis-directory

Brian Bushnell at JGI has a tool for masking by similarity and also low entropy regions, `BBMask`, could be worth a look: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbmask-guide/ (background thread:) http://seqanswers.com/forums/showthread.php?t=42552

We already have a wrapper around Picard's [`MergeSamFiles`](https://broadinstitute.github.io/picard/command-line-overview.html#MergeSamFiles), so is this a matter of dumping the header, altering it, and calling samtools' `reheader`? Or do we need to change the...

The documentation for V-Phaser II can be found here: http://software.broadinstitute.org/viral/docs/VPhaserII.pdf From the docs, the output files are described: ``` {ReferenceName}.fdr.var.txt – the result of interest, where strand bias test +...

It [appears](https://cromwell.readthedocs.io/en/develop/RuntimeAttributes/#bootdisksizegb) that with WDL 1.0 we can specify the bootsize as part of the `runtime` block: ``` runtime { bootDiskSizeGb: 50 } ```

@dpark01, maybe we want to de-dup before metagenomics classification as well—or at least have it as an option. @notestaff: Great! I'll hold off on integrating clumpify until after your PR...

@yesimon: Would you have time to add these functions? They would support later additions to automate db rebuild with new accessions. I like how easy [VirMet](https://github.com/ozagordi/VirMet/blob/master/virmet/common.py) makes it to rebuild...

dxWDL [has been updated](https://github.com/dnanexus/dxWDL/issues/150#issuecomment-484175141) to support WDL v1.0, so we can start updating our pipelines.

It sounds like Dockstore [is still working on support for WDL 1.0](https://github.com/ga4gh/dockstore/issues/2171).