I tested that there is no new warnings from nf-core linter caused by the changes.
I checked that I could build the docker image locally and start a container with it.
I did not cover details of the tools installed on the image as the dockerfile is an exact copy of the dockerfile on our previous repo (cqdg-denovo-nextflow) and was already thorougly tested in the past.
I did not covered github workflows logic as this is very complicated to test locally. If they malfunction, it should not break the pipeline code itself.
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
[x] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] 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.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).
I tested that there is no new warnings from nf-core linter caused by the changes. I checked that I could build the docker image locally and start a container with it.
I did not cover details of the tools installed on the image as the dockerfile is an exact copy of the dockerfile on our previous repo (cqdg-denovo-nextflow) and was already thorougly tested in the past.
I did not covered github workflows logic as this is very complicated to test locally. If they malfunction, it should not break the pipeline code itself.
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).