Lk paired tag naming collision

[ekiernan]

Description

This PR corrects a naming collision that occurs when multiple fastq lanes are used as input to the pipeline. As part of the demultiplexing step, we have to rename files so that software UPStools can perform trimming and preindex demultiplexing. This PR adds an additional renaming step using the basename of the original fastq after trimming to ensure that files do not have collisions in downstream workflow tasks.

A test run of this in on terra here: https://app.terra.bio/#workspaces/warp-pipelines/Multiome-test-workspace/job_history/4e1c5218-3873-4548-b2e6-8517a77b10a7

Checklist

If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.

• [ ] Did you add inputs, outputs, or tasks to a workflow?
• [ ] Did you modify, delete or move: file paths, file names, input names, output names, or task names?
• [ ] If you made a changelog update, did you update the pipeline version number?

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
PairedTag.wdl has not been changed and needs updating
atac.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
atac.wdl has not been changed and needs updating
Multiome.wdl has not been changed and needs updating
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
All WDLs and changelog files appear to be valid for this release.

[github-actions[bot]]

Remember to squash merge!

[github-actions[bot]]

Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/develop':
All WDLs and changelog files appear to be valid for this release.