Posted by Claude (AI assistant) on behalf of jmchilton — they did not author this text.
The workflow getting-started tutorial in docs/_running_intro.rst anchors the reader to a repository that has been archived for over four years.
$ git clone https://github.com/usegalaxy-eu/workflow-testing.git
$ cd workflow-testing/example3
usegalaxy-eu/workflow-testing is archived, last pushed 2021-02-19. Because archived repos stay readable, git clone still succeeds and example3 still resolves — so the tutorial is not broken, which is probably why this has gone unnoticed. But planemo's front-door introduction to running and testing workflows is built on a dead repository.
It is referenced four times in docs/_running_intro.rst (lines 5, 11, 12, and in the sample output on line 55).
Background
This was raised during review of #1426, where a maintainer noted that readers should be testing workflows from the IWC rather than usegalaxy-eu/workflow-testing, which "isn't very active or easily debuggable": #1426 (comment)
No action was taken at the time.
What needs deciding
Which IWC workflow replaces example3. The tutorial needs something that is small, fast to run on a locally hosted Galaxy, and ships both a job file and a test file, since the tutorial walks through planemo run and then planemo test against the same artifact.
Candidates worth sizing up:
workflows/read-preprocessing/short-read-qc-trimmingworkflows/data-fetching/parallel-accession-download
Whatever is chosen, the tutorial's sample outputs (the planemo run JSON on line 55 and the tutorial-tests.yml excerpt) have to be regenerated to match, not just re-pointed.
Related
The workflow getting-started tutorial in
docs/_running_intro.rstanchors the reader to a repository that has been archived for over four years.usegalaxy-eu/workflow-testingis archived, last pushed 2021-02-19. Because archived repos stay readable,git clonestill succeeds andexample3still resolves — so the tutorial is not broken, which is probably why this has gone unnoticed. But planemo's front-door introduction to running and testing workflows is built on a dead repository.It is referenced four times in
docs/_running_intro.rst(lines 5, 11, 12, and in the sample output on line 55).Background
This was raised during review of #1426, where a maintainer noted that readers should be testing workflows from the IWC rather than
usegalaxy-eu/workflow-testing, which "isn't very active or easily debuggable": #1426 (comment)No action was taken at the time.
What needs deciding
Which IWC workflow replaces
example3. The tutorial needs something that is small, fast to run on a locally hosted Galaxy, and ships both a job file and a test file, since the tutorial walks throughplanemo runand thenplanemo testagainst the same artifact.Candidates worth sizing up:
workflows/read-preprocessing/short-read-qc-trimmingworkflows/data-fetching/parallel-accession-downloadWhatever is chosen, the tutorial's sample outputs (the
planemo runJSON on line 55 and thetutorial-tests.ymlexcerpt) have to be regenerated to match, not just re-pointed.Related