This is using the simplest of workflows. I had to
remove the chromInfo part from the workflow, because the
path referenced would be changed dynamically and so the
job search wouldn't recognize this as being equivalent.
Also includes a simple test that runs cat1 three times,
the second time with `use_cached_job=False` (the default),
and the third time with `use_cached_job=True` and verifies
that the second output is different from the third, and that the
first and third output are identical.
This does not work at the moment, since we need to verify a jobs' input name,
dataset and metadata, for which we don't have an explicit trail. The only trace
is via the update_time (i.e if a input dataset hasn't been updated since the
job was created we know these were the actual parameters in use during the
execution of this job).
This specifically addresses the problem where some jobs of a mapped-over
collection have failed. Instead of filtering the failed collection and
restarting the workflow at this position (involving a lot of copy-paste ...)
the user can now limit the rerun to the problematic jobs and the workflow
should resume from there.
Should fix https://github.com/galaxyproject/galaxy/issues/2235.
This is one possible implementation, it would also be feasible to not
manipulate the original collection, but to copy the HDCA and then to replace
collection elements and replace all references for jobs that depend on the HDCA,
as we do for HDAs. This implementation seems simpler, but let me know if you
see problems with this approach.
This test runs a workflow whose first step fails, followed by a tool that uses
the first step's output as an input, which is behind a nested conditional. This
recapitulates the bug described in https://github.com/galaxyproject/galaxy/issues/5222.
- Update explicit stdio definitions as well as detect_errors-based definitions to allow this.
- Update runner code to allow resubmission in such cases.
- Add tests for creating a collection from a library.
- Add more class names to library GUI to improve selectors for tests.
- Automatically select whichever radio box makes sense in library collection builder dialog based on whether there is a selection or not.
Checking if pysam.index succeeds tests whether a file is coordinate sorted.
If pysam.index fails to index htslib writes to stderr and this fails set meta
tool. To prevent this we run this in a subprocess and discard stderr.
mvdbeek