Skip to content

Commit

Permalink
Additions
Browse files Browse the repository at this point in the history
  • Loading branch information
pjotrp committed Jan 3, 2019
1 parent e0194cb commit 0b32db3
Showing 1 changed file with 13 additions and 9 deletions.
22 changes: 13 additions & 9 deletions WORKFLOW.org
Original file line number Diff line number Diff line change
Expand Up @@ -876,14 +876,14 @@ CWL should become stronger and stronger. And with the growing support
any CWL user will get the benefit of capturing provenance graphs and
other goodies.

Beside improving the documentation, I suggest CWL gets an option for
checking determinism (run workflows multiple times and check results),
add support for native IPFS (a Python IPFS [[https://github.com/ipfs/py-ipfs-api][implementation]] exists) and
add some support for GNU Guix profiles - one single variable pointing
in the GUIX_PROFILE path - so it becomes even easier to create
Beside improving the documentation, I suggest CWL runners get an
option for checking determinism (run workflows multiple times and
check results), add support for native IPFS (a Python IPFS
[[https://github.com/ipfs/py-ipfs-api][implementation]] exists, alternatively [[https://github.com/ipfs/go-ipfs/blob/master/docs/fuse.md][IPFS fuse]] could be used) and add
some support for GNU Guix profiles - one single variable pointing in
the GUIX_PROFILE path - so it becomes even easier to create
deterministic software deployments that are built from source,
transparent and recreatable for eternity (which is a very long
time).
transparent and recreatable for eternity (which is a very long time).

It is particularly in these last two points of transparency and
recreatability that Docker falls short. A Docker image is a binary
Expand All @@ -901,14 +901,18 @@ source which means a workflow with tools can be audited and considered
more secure and (2) provides full transparency, recreatability (read
faithful reproducibility). With GNU Guix and CWL you don't need
Docker, though it is still possible to run Guix created Docker images
that also have these Guix advantages.
that also have these Guix advantages. Another advantage of Guix
containers over Docker containers is that they are [[https://github.com/pjotrp/guix-notes/blob/master/CONTAINERS.org][lighter]] and therefore
faster.

Finally, GNU Guix comes with its own workflow language [[https://www.guixwl.org/getting-started][GWL]] which
natively makes use of GNU Guix facilities. It may be worth looking
into because it is both simpler and more rigorous and can be combined
with CWL and in the future it may write CWL definitions. I am sure
I'll introduce a mix of GWL and CWL workflows in my pipelines in the
future.
future. Guix could also benefit from an online repository of channels
and pipelines similar to [[https://view.commonwl.org/workflows/github.com/nci-gdc/gdc-dnaseq-cwl/blob/0c1a40ea1efb1656644ccec0b7abe659539340e7/workflows/bamfastq_align/transform.cwl][view.commonwl.org]]. Very useful. Kudo's to the
creators.

* Extra notes

Expand Down

0 comments on commit 0b32db3

Please sign in to comment.