Create link to map on higlass server and don't duplicate files on higlass server

BethYates commented 11 months ago

Check if data exists already exists on the Higlass server before adding it.Removes file if already present before re-uploading, outputs uuid of uploaded files for use when creating link to higlass server. Generates link to the uploaded higlass map.

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
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile 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).

github-actions[bot] commented 11 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit 3ebeb24

+| ✅ 130 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   1 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.1.0'`` ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-genomenote_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - 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BethYates commented 11 months ago

A new module was added to generate the link to the higlass map. It uses the python request module to make a post request to the higlass API with the specified viewconfig. This request returns a uid for the view config which can then be used to form the link to the map.

github-actions[bot] commented 10 months ago

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gq1 commented 9 months ago

Nothing to do with this PR, just wondering why the Github CI test being removed on Pull Request? I can't see any CI Test being run on Docker profile for this PR.

BethYates commented 9 months ago

Nothing to do with this PR, just wondering why the Github CI test being removed on Pull Request? I can't see any CI Test being run on Docker profile for this PR.

Is this because the merge is between my feature branch and the public_dev branch rather than being to the main dev branch?

gq1 commented 9 months ago

Every time I start the pipeline, there is a warning message not sure which line yet. Can we remove it? WARN: The operatorfirstis useless when applied to a value channel which returns a single value by definition

gq1 commented 9 months ago

Nothing to do with this PR, just wondering why the Github CI test being removed on Pull Request? I can't see any CI Test being run on Docker profile for this PR.

Is this because the merge is between my feature branch and the public_dev branch rather than being to the main dev branch?

No, these lines being modified in the upstream. Currently the CI test only can be triggered manually. https://github.com/sanger-tol/genomenote/blob/c6e85036d27d59a9610e5d1c2aedb67f7046dbd1/.github/workflows/ci.yml#L3

gq1 commented 9 months ago

I tried nextflow run genomenote/main.nf -profile singularity,sanger,test on tol farm 3 times.

FASTK_FASTK always failed in the first attempt and stuck on the second attempt.

Because this PR is mainly for higlass loading. Tried the following again: nextflow run genomenote/main.nf -profile singularity,sanger,test -resume --upload_higlass_data --higlass_data_project_dir /asg/algae_gq2 --higlass_kubeconfig /nfs/users/nfs_g/gq2/tol-it-dev-config-openlab

The job again was stuck on FASTK_FASTK but passed the higlass_loading step successfully.

I can find the output file from the work directory with higlass link, uoEpiScrs1_T3_higlass_link.csv http://genome-note-higlass.tol-dev.sanger.ac.uk/l/?d=GCA_946965045_2_uoEpiScrs1_T3

I can see the file in the publish dir and in the results folder.

And the link works and I also can see the project and tilesets I created on higlass server.

Screenshot 2024-02-02 at 11 31 37

gq1 commented 9 months ago

@BethYates can run the test without sanger profile. I tried nextflow run genomenote/main.nf -profile singularity,test

failed on SANGERTOL_GENOMENOTE:GENOMENOTE:CONTACT_MAPS:SAMTOOLS_VIEW (uoEpiScrs1_T3)

with the following error message:

Caused by:
  Process requirement exceeds available CPUs -- req: 2; avail: 1

gq1 commented 9 months ago

I tried nextflow run genomenote/main.nf -profile singularity,sanger,test -resume --upload_higlass_data --higlass_data_project_dir /asg/algae_gq2 --higlass_kubeconfig /nfs/users/nfs_g/gq2/tol-it-dev-config-openlab again.

I can see the old tilesets being deleted from the server and the file systems. And then same link being generated with the new tilesets.

BethYates commented 9 months ago

Every time I start the pipeline, there is a warning message not sure which line yet. Can we remove it? WARN: The operatorfirstis useless when applied to a value channel which returns a single value by definition

I'll address this when I do the merge from the dev branch to the public dev branch after the PR is merged

BethYates commented 9 months ago

Nothing to do with this PR, just wondering why the Github CI test being removed on Pull Request? I can't see any CI Test being run on Docker profile for this PR.

Is this because the merge is between my feature branch and the public_dev branch rather than being to the main dev branch?

No, these lines being modified in the upstream. Currently the CI test only can be triggered manually.

https://github.com/sanger-tol/genomenote/blob/c6e85036d27d59a9610e5d1c2aedb67f7046dbd1/.github/workflows/ci.yml#L3

Ah, I think the public_dev branch was made before the CI testing was set up correctly for this repo. I plan to merge dev into this branch which should hopefully fix this

sanger-tol / genomenote