Resolve "Change Single Read to Single End for submitted endness"

Cumulative branch for v2.0.0

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!
• [ ] Documentation in docs is updated
• Replace dag.png with the most recent CI pipeline integrated_pe artifact
• [ ] Replace software_versions_mqc.yaml with the most recent CI pipeline generateVersions artifact
• [ ] Replace software_references_mqc.yaml with the most recent CI pipeline generateVersions artifact
• CHANGELOG.md is updated
• [ ] README.md is updated
• [ ] LICENSE.md is updated with new contributors
• [ ] Docker images moved to production release and changed in pipeline
• [ ] Docker images used in the CI unit tests match those used in pipeline

• Close issue
  Closes #110 (closed) Closes #114 (closed) Closes #115 (closed) Closes #70 (closed) Closes #111 (closed) Closes #112 (closed) Closes #100 (closed) Closes #95 (closed)

/cc @ghenry @venkat.malladi

changed milestone to %v2.0.0

added Test critical data-hub pipeline labels

added 4 commits

• a19f61d1 - Convert strandedness from yes/no to t/f
• 03f13a82 - Remove unnecessary RID output parsing
• f4e88555 - Add blank mRNA_QC on data fail
• 77410b76 - Merge data error pre-Execution run

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added 1 commit

• a503d1e2 - Change logic for uploadOutputBag

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• c4c258bf - Temporarily change CI integration tests to use dev server (staging doesn't have model changes)

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• c2a7f9b0 - Update parseMetadata ci test

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• ddc9ef20 - Fix getRef use of new spike values

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added 3 commits

• b15b2201 - URLify hatrac location for outputBag
• b5569b5b - Update create test data with new metadata model
• 42785f19 - Update create test data with new metadata model

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• b390a5e5 - Excape bash vars

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• 0511ac1a - Double excape slash

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• 59cb654a - Add force params for stranded and spike

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• c03c60c9 - Add qutes to echo

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• 4d50fe8f - Fix qutes to echo

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• e7024f45 - Add missing excapes

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• a3d8f200 - Remove unnecessary excape

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• 57529bc9 - Fix new force var names

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• ecd4e76f - Add new py tests for integration and override

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• 6b085ad6 - Remove extra quote

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• 4f9bc352 - Fix echo line
• 349cbde4 - Change replicate for SE integration

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• 37bec34c - Revert SE integration test and server for all integrations

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added 1 commit

• 14b8fc1d - Fix bracket

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• a32879db - Update pytests

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added 2 commits

• 09dd7af3 - Fix stranded variable
• 1d912493 - Update pytest to utilize params

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added 1 commit

• df96927b - Make tracking upload option

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• 502328a7 - Fix params

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• 8a1299d4 - Fix aggrQC if brackets

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added 1 commit

• 6e617062 - Update reps used for override metadata

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• 04c81525 - Fix stranded override

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• 2ddefb95 - Change replicates for metadata overrides

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• 63fbe5e4 - Fix spike override test
• 329dc950 - Fix metadata echo

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added 2 commits

• a7d4aa13 - Update DAG
• b1cdf286 - Try excaping tabs for metadata override for report

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marked the checklist item This comment contains a description of changes (with reason) as completed

marked the checklist item Replace dag.png with the most recent CI pipeline integrated_pe artifact as completed

marked the checklist item CHANGELOG.md is updated as completed

marked the checklist item *Close issue* as completed

added 2 commits

• 8859d7e9 - Add multiqc html to ci artifacts for override tests
• 6961db25 - Update version to 2.0.0rc01

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marked this merge request as ready

marked the checklist item If you've fixed a bug or added code that should be tested, add tests! as completed

approved this merge request

enabled an automatic merge when the pipeline for 6961db25 succeeds

aborted the automatic merge because source branch was updated

added 1 commit

• 37a1345e - Convert blank nan submitted metadata to No value

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approved this merge request

enabled an automatic merge when the pipeline for 37a1345e succeeds

aborted the automatic merge because source branch was updated

added 2 commits

• f36d728b - Fix spike override ci pytest
• 0bb07de4 - Move spike/stranded override to infer (like species), not submitter

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added 2 commits

• ced21083 - Fix getRef for spike
• 762f3ba7 - Update dag

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approved this merge request

enabled an automatic merge when the pipeline for 762f3ba7 succeeds

aborted the automatic merge because source branch was updated