Review software for upgrades

[chrisamiller]

Prior to pushing out a 2.0 release and re-benchmarking, we should review key software components and bump versions to the latest and greatest when it makes sense. These don't necessarily need to be updated, but if we are going to do so, before a release is the right time.

A preliminary list of software to check, based on docker images:

• smoove
• somalier
• bedtools
• cnvkit
• vatools
• kallisto
• star
• starfusion
• biscuit
• manta
• strelka
• picard
• pizzly
• sambamba
• samtools
• vep
• vt
• cellranger
• hisat
• stringtie
• bcftools
• fgbio
• mutect
• pvactools

Feel free to add things I've missed below, or to check these off when you've confirmed that a) they have been upgraded or b) they don't need to be (add comments confirming below)

[chrisamiller]

Notes on a few of these. Switching to "official" docker containers or those in bioconda/biocontainers seems like a good plan, especially when it reduces dependency on our own images or dockerhub.

#kallisto:
quay.io/biocontainers/kallisto:0.46.1--h4f7b962_0
#should be no index change - test

#hisat
quay.io/biocontainers/hisat2:2.2.1--he1b5a44_2

#star-fusion
quay.io/biocontainers/star-fusion:1.9.0--1

#stringtie:
quay.io/biocontainers/stringtie:2.1.2--h7e0af3c_1

#biscuit:
#may have some param changes (?)
#new URL https://github.com/huishenlab/biscuit
quay.io/biocontainers/biscuit:0.3.16.20200420--h2b0c03c_2

#somalier
#Looks like minor bugfixes. A version bump and a quick sanity check on a pair of bams oughta be fine
#hosted on dockerhub - brentp/somalier, seems like we should create our own to remove dependency on other people's dockerhub, at least

#mutect:
seems like a bump to newest version 4.1.8.1 would be easy/fine - couple of bugfixes

#picard:
#seems like these are all bugfixes, just a bump is probably fine
quay.io/biocontainers/picard:2.23.3--0

#pvactools:
#@susannasiebert has upgraded CWLs with the new pVACtools version.
dockerPull: "griffithlab/pvactools:2.0.1"

[chrisamiller]

Cellranger has a 4.0 release with substantial improvements in speed (and no obvious changes in parameters). @apaul7 made an internal image at registry.gsc.wustl.edu/alex.paul/cellranger:4.0.0 and the executable is /apps/cellranger-4.0.0/cellranger. I think it's a clean upgrade, but needs testing

[apaul7]

updated the cellranger cwls to 4.0.0 with #968

[chrisamiller]

Assigments:
bedtools - @smk5g5
cnvkit - @johnegarza
kallisto - @chrisamiller
star - @sridhar0605
starfusion - @sridhar0605
biscuit - @chrisamiller
manta - @apaul7
pizzly - @chrisamiller
samtools - @smk5g5
vt - @johnegarza
hisat - @chrisamiller
stringtie - @chrisamiller
bcftools - @smk5g5
fgbio - @tmooney
pvactools - @gschang

[chrisamiller]

• Pizzly is fine
• I put in a PR to bump the kallisto version
• with biscuit, we're going to stay on 0.3.8 for now and wait for the 1.0 release that has some new features and breaking changes (probably early next year)

[apaul7]

updated manta to v1.6.0 in #992

[gschang]

As a heads-up for this milestone, we recently got a major release of pVACtools by @susannasiebert. As discussing with @jhundal, we plan to test this new release with clinical cases in order to upgrade the immuno workflow.

[New update on Feb 24]
Susanna has worked out pVACseq upgrade by merging PR #1003. I am going to run this new pVACtools with several clinical cases.

[apaul7]

I don't think VT needs to be updated.
The image we have in repo is quay.io/biocontainers/vt:0.57721--hf74b74d_1 has version vt v0.5772-60f436c3
The latest image from quay has tag 0.57721--h41af197_4 which contains the same version(vt v0.5772-60f436c3)