Closed DLBPointon closed 11 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 913bf8b
+| ✅ 133 tests passed |+
#| ❔ 15 tests were ignored |#
!| ❗ 13 tests had warnings |!
@DLBPointon Do you want to fix the CI tests in this pipeline too?
@DLBPointon Do you want to fix the CI tests in this pipeline too?
I will be. I'll ask Guoying about it tomorrow, as it's all tower stuff, we are in an ascc Hackathon at the minute.
The tower agent was down two days ago. I re-run the job and submitted it to Tower successfully.
But the pipeline failed to run. https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/4Mp053V8l2TU1H
ERROR ~ ERROR: Validation of pipeline parameters failed!
-- Check 'nf-4Mp053V8l2TU1H.log' file for details
ERROR ~ * --input: string [/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta] does not match pattern ^\S+\.fa$ (/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta)
-- Check 'nf-4Mp053V8l2TU1H.log' file for details
Exiting!
The tower agent was down two days ago. I re-run the job and submitted it to Tower successfully.
But the pipeline failed to run. https://tower.nf/orgs/sanger-tol/workspaces/github-ci/watch/4Mp053V8l2TU1H
ERROR ~ ERROR: Validation of pipeline parameters failed! -- Check 'nf-4Mp053V8l2TU1H.log' file for details ERROR ~ * --input: string [/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta] does not match pattern ^\S+\.fa$ (/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta) -- Check 'nf-4Mp053V8l2TU1H.log' file for details Exiting!
Hi Guoying, Thanks for having a look, I've fixed the issue in: https://github.com/sanger-tol/curationpretext/pull/13 The Schema just needed updating, I also changed the outdir value other wise it would constantly come back as null in tests.
Hi Guoying, Thanks for having a look, I've fixed the issue in: #13 The Schema just needed updating, I also changed the outdir value other wise it would constantly come back as null in tests.
Can you re-trigger the Github action run to test?
Morning @priyanka-surana, @gq1 Looks like all tests including Tower have been completed successfully.
Hi @priyanka-surana, Can this now be approved?
Hi @priyanka-surana, Can this now be approved?
Never mind this should wait on #14
I tried the test
profile on the farm as well and got the same error message.
Can we have the instruction as @muffato did to TreeVal to have some instructions to download the test file from S3 and replace all the github path to the local path?
I can see the test profile is set for GitHub, which profile should I be using to test the subset and full datasets? Thanks.
I also tried the test_full
profile directly on the farm, it works fine. This profile already passed on the farm via Github action and Tower.
Thanks both @gq1 and @priyanka-surana. I've submitted fixes, they are on #14. usage now contains information on amending the test.config.
Closes #6
Release ready pipeline!