Closed muffato closed 9 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 54f5568
+| ✅ 129 tests passed |+
#| ❔ 18 tests were ignored |#
!| ❗ 4 tests had warnings |!
The only comment is that the blastn databases for running the small and full tests are about 70 MB in size, if these files are too large to be part of the repo then the remote paths for them have to be updated accordingly in this branch and in the blastn branch.
That's absolutely fine. I actually think the .dmnd
files should be moved from assets/
to remote paths as well. Even if they're small, it's not the sort of things that should really be kept in the code repository.
@muffato Any other changes to this PR. Otherwise I would like to merge this into #83 and run the tests.
@priyanka-surana I moved the .dmnd
files to S3 and updated the test config. Ready to merge !
The purpose of this pull-request is to reinstate the CI tests on GitHub. The main trick is to simply add some steps to the CI workflow to download the necessary databases (NCBI Taxonomy and BUSCO).
At the same time, I recreated the reduced BUSCO databases with a script that is now under
/lustre/scratch123/tol/resources/nextflow/busco
. The new databases have 10 genes (or less) that are known hit and 5 genes that have no hit. Like in https://github.com/sanger-tol/genomenote/pull/77 I change the metauk parameters to make BUSCO even faster.Other changes:
/lustre/scratch123/tol/resources/nextflow/test-data
, which is fully synchronised with the S3 server.pipeline_info/blobtoolkit
, as per our new convention.docker.io/
prefix to a few containers as the default now isquay.io
. This is actually the result of getting the CI to work ! We had not spotted the error because we only use Singularity on the farm.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).