Allow to run the post processing pipeline in stub mode in the github workflow ci.yml.
We adjusted a few things to make this work:
fix bugs in test sample sheet and make it cover both WGS an WES sequencing types
complete the test profile and add missing required parameters in schema
adjusted the github workflow command to add the -stub option
We also take the oppotunity to do a bit of cleanup on the github workflow files:
align trigger rules with ferlab git flow (sadly had to disable 2 linter tests to allow this)
use the same nextflow version as in production (23.10.1)
Other changes:
We realized while testing on juno that the docker image for process writemeta was missing, so we add it in nextflow.config
We also realized that the changelog was not displayed correctly in the UI. We fixed that.
Fix bug with extra java arguments in process CombineGVCF
Test description
We make sure that github workflow is executed correctly on this PR
Local tests:
We run nf-core lint and check that no test is failing and that there are no new warnings caused by the changes here. Actually, we got rid of 3 warnings (TODO keywords found in doc).
Check that the following commands work locally:
nextflow run main.nf -stub -profile test,docker
nextflow run main.nf -stub -profile test
I started from remi antoine's test dataset. I found 2 bugs while doing that:
gvcf file extension .g.vcf.gz not supported
For some processes, it is assumed that both extra arguments and extra java options are passed via ext.args, which does not work.
I think that they should be addressed in dedicated PRs. For the first bug, I simply copied my input file into a new file with extension .gvcf. For the second bug, I commited a fix specifically for the process causing problem for my test, but the problem is present in other processes as well.
PR checklist
[x] 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
[x] Make sure your code lints (nf-core lint).
[x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[x] Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[x] CHANGELOG.md is updated.
[x] README.md is updated (including new tool citations and authors/contributors).
Allow to run the post processing pipeline in stub mode in the github workflow ci.yml.
We adjusted a few things to make this work:
We also take the oppotunity to do a bit of cleanup on the github workflow files:
use the same nextflow version as in production (23.10.1)
Other changes:
Test description
We make sure that github workflow is executed correctly on this PR
Local tests:
nf-core lintand check that no test is failing and that there are no new warnings caused by the changes here. Actually, we got rid of 3 warnings (TODO keywords found in doc).Tests on juno:
Was able to run a job successfully:
I started from remi antoine's test dataset. I found 2 bugs while doing that:
I think that they should be addressed in dedicated PRs. For the first bug, I simply copied my input file into a new file with extension .gvcf. For the second bug, I commited a fix specifically for the process causing problem for my test, but the problem is present in other processes as well.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).