BUSCO was run three times because it failed twice with the exit code 140, which is RUNLIMIT.
The details view show that all were actually run with a maximum runtime of 2 hours.
On one hand it's interesting that 2 hours is probably fine as a limit, since it dit eventually complete in about half of it. On the other hand, I was meaning to take task.attempt into account in every formula. In fact, This BUSCO runtime is the only one where I forgot to include task.attempt !
This PR simply adds task.attempt as a multiplier.
PR checklist
[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
This pull-request addresses an issue I've found when inspecting the last full test run: https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/1JKq8hhG0lujva
BUSCO was run three times because it failed twice with the exit code 140, which is RUNLIMIT.
The details view show that all were actually run with a maximum runtime of 2 hours. On one hand it's interesting that 2 hours is probably fine as a limit, since it dit eventually complete in about half of it. On the other hand, I was meaning to take
task.attempt
into account in every formula. In fact, This BUSCO runtime is the only one where I forgot to includetask.attempt
!This PR simply adds
task.attempt
as a multiplier.PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).