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

[BethYates]

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]]

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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Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - 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[BethYates]

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]]

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

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[gq1]

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]

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]

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]

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]

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.

[gq1]

@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]

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]

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]

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