Np add metadata.txt file to build indices

[nikellepetrillo]

Description

This PR adds a task to the BuildIndices script that will build a text file with:

• the pipeline-version
• the file paths for the inputs references that are modified or used
• the md5sums on all input files and output files
• the date of workflow run (time stamp)
• the workflow id

example .txt file looks like:

Date of Workflow Run: 2024-11-25T21:48:18Z

Input Files and their md5sums:
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/human/gencode.v43.primary_assembly.annotation.gtf : e00b8eb11ad5a2caaa252e0160ef350c
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/human/GRCh38.primary_assembly.genome.fa : 49bdb80d21a64dcb16acfc941843356e
/cromwell_root/fc-c40ec8a8-d60f-42f7-be36-3986b475190a/Biotypes.tsv : ad3206cda213d77fe39dc92bb02085c4

Output Files and their md5sums:
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/submissions/28f6a552-31b3-43d8-81a8-d409a7d87662/BuildIndices/e3bfb17d-9322-4b7f-b4d2-895cb011e10f/call-BuildStarSingleNucleus/cacheCopy/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar : 06fdf87249b42966973d8e4d9399ba40
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/submissions/28f6a552-31b3-43d8-81a8-d409a7d87662/BuildIndices/e3bfb17d-9322-4b7f-b4d2-895cb011e10f/call-BuildStarSingleNucleus/cacheCopy/modified_v43.annotation.gtf : 42d9352fcf93ff18cbe2aa074072f211
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/submissions/28f6a552-31b3-43d8-81a8-d409a7d87662/BuildIndices/e3bfb17d-9322-4b7f-b4d2-895cb011e10f/call-CalculateChromosomeSizes/cacheCopy/chrom.sizes : f94face851cb2129ab423f54db04fa0c
/cromwell_root/fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378/submissions/28f6a552-31b3-43d8-81a8-d409a7d87662/BuildIndices/e3bfb17d-9322-4b7f-b4d2-895cb011e10f/call-BuildBWAreference/cacheCopy/bwa-mem2-2.2.1-Human-GENCODE-build-GRCh38.tar : 3702fd2919568b5ddb03c57c535d4ee0

Workspace Bucket: fc-e7f669fe-5a5c-4a8c-ad02-3b69105d0378
Submission ID: 28f6a552-31b3-43d8-81a8-d409a7d87662
Workflow ID: e3bfb17d-9322-4b7f-b4d2-895cb011e10f

---

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 team by tagging @broadinstitute/warp-admins 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]

Remember to squash merge!

[github-actions]

🔍Version Validation Results:

Comparing versions and changelogs for pipelines that differ from the versions on 'origin/staging':
BuildIndices.wdl has not had its version updated
Some WDLs or changelog files need updating. See output for details.
validation_failed

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
BuildIndices.changelog.md has not been changed and needs to be updated
Some changelog files need updating. See output for details.
validation_failed

[github-actions]

Remember to squash merge!

[github-actions]

🔍Changelog Validation Results:

Comparing changelogs for pipelines that differ from the versions on 'origin/develop':
All changelog files are valid for this release.

[github-actions]

🔍Version Validation Results:

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

[ekiernan]

Thank you so much, Nikelle. This looks great!

[nikellepetrillo]

Thank you so much, Nikelle. This looks great!

thanks liz! sorry, i accidentally requested you to re-review :(