There is no Directory type in CWL. The one instance of this,
vep_cache_dir
, has been changed to vep_cache_dir_zip
and expects a
zipped file of the dir, where the zip contains the contents of the dir
not the dir itself.
As far as I can tell there's no equivalent of
"InitialWorkDirRequirement" from CWL in WDL. Where we use this to
create a script to execute, that scripts contents have been moved to
the command
block of their task. No difference to the caller.
Input files must prefix each argument with the name of the workflow
they're going to run, because a WDL file can contain multiple
workflows or pass inputs over a layer if they aren't propagated
through in the definition. e.g. to call workflow somaticExome
with
input foo
, yaml key must be somaticExome.foo
WDL does not allow relative imports on the root file, so you'll need a
local copy that strips the leading ../
from each import. In CWL a
similar issue happened but had a workaround of zipping the deps in a
tricky way to allow it. WDL bans it outright.
Various tools need space allocation for their outputs
Actually use custom annotations that are passed in
Docker version update from 0.9.5 to 0.9.8 causes a regression and we
need a solution because it enables CRAM support. Specifically
permissions to write are denied for commands like mv
, touch
, and
generated index files within the script. It does work locally, so
troubleshooting is probably required before filing a report to CNVkit
owners.
Timing diagrams for the same run between cloud and cluster show that the cloud runs about 50% longer than the cluster. Localization accounts for a portion of this, but task runtimes are also slower on the cloud.