Release 5.0.0

[yashpatel6]

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  metadata.yaml and the manifest block in the nextflow.config as part of this pull request, am listed
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• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample.

Updating tests for release 5.0.0; updating documentation

Testing Results

All NFTest cases were run:

• output: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-release-5.0.0/
• logs: /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/yashpatel-release-5.0.0/logs

[yashpatel6]

@raagagrawal @nkwang24 @graceooh For README review

[raagagrawal]

lgtm

[nwiltsie]

In broad strokes this looks good - I have a few minor comments, but I'd also like to test this out before I formally approve.

[yashpatel6]

In broad strokes this looks good - I have a few minor comments, but I'd also like to test this out before I formally approve.

Definitely, you should be able to run any of the test cases; the pipeline-specific tests and test-metapipeline-DNA should run on any node higher than an F2 and the other two cases (test-metapipeline-DNA-batch and test-metapipeline-DNA-fastq-input) should run on an F2 node (those cases include the submission step where the main job submits jobs to other nodes)

[nwiltsie]

Ha, I was literally just typing out my comment that that test was failing for me!

[yashpatel6]

Ha, I was literally just typing out my comment that that test was failing for me!

Yeah I ran the test previously before I updated the status checking part in the tests, but should be fixed now!

[tyamaguchi-ucla]

Looks good to me as long as all the tests work. I've added some minor comments/suggestions.

[nwiltsie]

A few points:

1. Several of the tests have hardcoded references to /hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir, and I was unable to write to some directories in that folder. We need to clean up that directory and set the sticky bit to ensure that new folders are writable.
2. Several tests failed but I got a "COMPLETED, ExitCode 0" email from Slurm... I might have configured something strange, but I wanted to call it out in case there's something odd about either NFTest or the bubbling up of errors in the metapipeline:

│2023-10-27 07:35:32,359 - NextFlow - INFO - ERROR ~ Error executing process > 'create_config_metapipeline_DNA (3)'                                                                                │
│2023-10-27 07:35:32,359 - NextFlow - INFO -                                                                                                                                                       │
│2023-10-27 07:35:32,359 - NextFlow - INFO - Caused by:                                                                                                                                            │
│2023-10-27 07:35:32,359 - NextFlow - INFO -   Unable to create directory=/hot/software/pipeline/metapipeline-DNA/Nextflow/development/unreleased/common_work_dir/c0/5c80a178c5f73d067a310395e3df5b│
│2023-10-27 07:35:32,359 - NextFlow - INFO -                                                                                                                                                       │
│2023-10-27 07:35:32,359 - NextFlow - INFO -                                                                                                                                                       │
│2023-10-27 07:35:32,359 - NextFlow - INFO -  -- Check '/hot/user/nwiltsie/logs/nextflow-20231027T141018Z.log' file for details                                                                    │
│2023-10-27 07:35:32,359 - NextFlow - INFO -                                                                                                                                                       │
│2023-10-27 07:35:32,422 - NFTest - ERROR -  [ failed ]

[nwiltsie]

So one test failed due to #145 , but that shouldn't hold up this PR.