Erin remove nf core

[erinyoung]

Because the latest version of IRMA isn't on CONDA, I removed CONDA from the workflow.
I removed all github action (GA) testing that dealt with AWS - because we don't have that capacity.
I also removed all references to the walkercreek slack channel in nf-core's slack space, because that doesn't exist.
I changed all the nf-core/walkercreek instances to UPHL-BioNGS/walkercreek.

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- [ ] If necessary, also make a PR on the nf-core/walkercreek branch on the nf-core/test-datasets repository.
• 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]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 984161e

+| ✅  16 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• files_unchanged - files_unchanged
• actions_awstest - actions_awstest
• multiqc_config - multiqc_config
• modules_structure - modules_structure

✅ Tests passed:

• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (119 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json

Run details

• nf-core/tools version 2.7.2
• Run at 2023-12-07 19:16:26

[tives82]

I have made the necessary changes to pass lint testing and complete the PR checklist. I have tried to be descriptive on the commits.

[erinyoung]

This looks great!

Thank you for fixing this!!!

It looks like I accidentally added in all the @eaDir/* directories that mac creates and I can't delete them. Can you delete them?

[tives82]

This looks great!

Thank you for fixing this!!!

It looks like I accidentally added in all the @eaDir/* directories that mac creates and I can't delete them. Can you delete them?

Oh, I was wondering where those @eadir directories come from. I probably added to the number of them as well. I think I have deleted them all now. When I run the below command, they are no longer listed.
find . -name "@eaDir" -type d

[tives82]

This looks great!
Thank you for fixing this!!!
It looks like I accidentally added in all the @eaDir/* directories that mac creates and I can't delete them. Can you delete them?

Oh, I was wondering where those @eadir directories come from. I probably added to the number of them as well. I think I have deleted them all now. When I run the below command, they are no longer listed. find . -name "@eaDir" -type d

I also removed a temporary SMB file from the images directory that for whatever reason wasn't previously deleted.

[erinyoung]

Awesome! They still look like they are part of this repo, though. If all fails, we can merge this and then delete the files later.