Closed BethYates closed 10 months ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 2a457f2
+| ✅ 130 tests passed |+
#| ❔ 20 tests were ignored |#
!| ❗ 1 tests had warnings |!
Update_higlass_server module expects to be passed two files a '.mcool' file and a '.bedpe' file. The actual files that get uploaded are copied to the directory specified by the 'higlass_upload_directory' param by the publishDir directive used by the module that produces each file type. This seems a bit of a hacky way to do it but it works. The publishdir directive for Update_higlass_server.nf means that we still get the expected files in the results/contact_maps directory.
When I finished testing there were two copies of each file type in a directory named "GCA_946965045.2" you can see the data here http://genome-note-higlass.tol-dev.sanger.ac.uk/l/?d=NHOYirQrTn-oOWiQcakVPw Each time a test is run a new copy of each file will be uploaded.
I can confirm that it works and I could do a test_full
run of the pipeline and see the contact map at http://genome-note-higlass.tol-dev.sanger.ac.uk/l/?d=P4JitQ-fQEuXfxrack5XBA
I'm proposing some improvements in #79
I can confirm that it works and I could do a
test_full
run of the pipeline and see the contact map at http://genome-note-higlass.tol-dev.sanger.ac.uk/l/?d=P4JitQ-fQEuXfxrack5XBA
You generated the view link manually, not by the pipeline? Will is still trying to generate the links automatically
You generated the view link manually, not by the pipeline? Will is still trying to generate the links automatically
Yes, I created the link manually. Creating the link automatically is out of scope for this ticket (TOLIT-427) but it's something we should consider part of the epic (TOLIT-1601)
I do not have a
kubeconfig
so that step was skipped. I think @gq1 should test this. Otherwise all the steps ran successfully with thetest
profile.
@muffato has tested all the uploading.
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).