Daniel Park

In light of the official [EOL date](https://www.python.org/dev/peps/pep-0373/) for Python 2 at the end of this year, and the fact that most of our critical python dependencies seem to be [on...

It's probably about time to make sure we add support for zstd throughout our various bits of code for databases (such as `read_utils.py extract_tarball`, among other places) and flowcell tarballs...

rnaSPAdes sometimes does not emit transcripts.fasta

1

Apparently in [some scenarios](https://platform.dnanexus.com/projects/FJ3g57j0fBX7Ggxv6ZPjyjK2/monitor/analysis/FJB2VK80fBXJbkZ1FX1B4Kyx), the SPAdes assembler in RNA mode does not output a transcripts.fasta file at all. Not sure if this is it's normal behavior in empty output scenarios...

update and test Cromwell 32 with Google PAPI v2

2

[Cromwell version 32](https://github.com/broadinstitute/cromwell/releases/tag/32) starts the transition from PAPIv1 to PAPIv2 and signals the future deprecation some of the old "JES" terminology (the predecessor to PAPI). Our current template [Cromwell config...

Add automated blastx-like LCA of post-spades contigs to demux_plus.wdl

1

Partly motivated by ongoing analyses @tomkinsc is working on, it would be useful to consider a way of automating a way to taxonomically classify the SPAdes-based contigs that are already...

Change krona wrapper to read from summary report instead of read report

8

In our current invocations in the WDL workflow, we run kraken, and then krona, on a bunch of samples to save on DB staging time and such. Currently, the krona...

Since Broad legal has given their blessing, we should: - add the full GATK 3.8 jar to the bioconda package (get rid of the register command) - remove all of...

tolerate single-end reads throughout pipeline

14

All throughout the pipeline, there are places that assume paired-end reads, and it's mostly how we wrap underlying tools, probably not the underlying tools themselves. For example, BAM->fastq conversion for...

pysam mostly works with Travis, except a few of the functions that embed samtools functionality (like pysam.view) which do some weird redirection of stdin/stdout, but Travis does some weird redirection...

create bam merger for unaligned reads

2

Create a script that merges BAM files of unaligned reads together while also presenting the opportunity to rewrite certain bits of commonly rewritten metadata, like the sample name and library...