Closed DSchreyer closed 1 year ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 48b449b
+| ✅ 157 tests passed |+
#| ❔ 2 tests were ignored |#
!| ❗ 2 tests had warnings |!
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Hi @jluebeck and @SPPearce , About the pipeline update. I included your suggestions and updated the pipeline.
PrepareAA is still not included and needs to be included as soon as the docker container was generated. @pditommaso noted that nextflow has a wave option to generate containers on-the-fly. I will try to include it in this release so I will wait to merge until it is clear how I can implement wave into the pipeline.
@SPPearce Let me know if you identified issues or changes that need to be implemented. I hope I addressed all your change request for a version release.
I now stopped using wave
and have fallen back to docker when talking about PrepareAA. PrepareAA will not yet be implemented, but will be implemented in the next release which will hopefully follow soon after this one. The only issue is, as I mentioned before, the docker container that is required for it to fully function with singularity and docker.
@SPPearce Let me know if you identified issues or changes that need to be implemented. I hope I addressed all your change request for a version release.
I now stopped using
wave
and have fallen back to docker when talking about PrepareAA. PrepareAA will not yet be implemented, but will be implemented in the next release which will hopefully follow soon after this one. The only issue is, as I mentioned before, the docker container that is required for it to fully function with singularity and docker.
I think most of my comments will be best resolved once the whole of AmpliconArchitect is on bioconda, that'll move a lot of the scripts from the pipeline here to just being present in the container.
@SPPearce Let me know if you identified issues or changes that need to be implemented. I hope I addressed all your change request for a version release. I now stopped using
wave
and have fallen back to docker when talking about PrepareAA. PrepareAA will not yet be implemented, but will be implemented in the next release which will hopefully follow soon after this one. The only issue is, as I mentioned before, the docker container that is required for it to fully function with singularity and docker.I think most of my comments will be best resolved once the whole of AmpliconArchitect is on bioconda, that'll move a lot of the scripts from the pipeline here to just being present in the container.
I agree. Thanks for reviewing and all your suggestions!
v1.0.3 - [2023-03-23]
Added
Fixed
Dependencies
Deprecated
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).