The Big Merge

[DLBPointon]

Closes #6

Release ready pipeline!

[DLBPointon]

@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.

[gq1]

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!

[DLBPointon]

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: #13
The Schema just needed updating, I also changed the outdir value other wise it would constantly come back as null in tests.

[gq1]

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?

[DLBPointon]

Morning @priyanka-surana, @gq1
Looks like all tests including Tower have been completed successfully.

[DLBPointon]

Hi @priyanka-surana,
Can this now be approved?

[DLBPointon]

Hi @priyanka-surana, Can this now be approved?

Never mind this should wait on #14

[priyanka-surana]

I tried the test profile and it fails for me.

nextflow run . -profile test,singularity --outdir results -ansi-log false
ERROR ~ Unable to read script: '/lustre/scratch123/tol/teams/tolit/users/ps22/pipelines/sanger-tol-curationpretext_dev/dev/./workflows/curationpretext_allf.nf' -- cause: /home/runner/work/curationpretext/curationpretext/TreeValTinyData/genomic_data/pacbio

I can see the test profile is set for GitHub, which profile should I be using to test the subset and full datasets? Thanks.

[gq1]

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.

[DLBPointon]

Thanks both @gq1 and @priyanka-surana.
I've submitted fixes, they are on #14. usage now contains information on amending the test.config.

[DLBPointon]

#14 is now merged

[priyanka-surana]

LGTM 👍🏼