Lk pd 2562 bam header

[ekiernan]

This PR adds the cloud path to the reference files used for alignment to the BAM headers for Multiome, Pairedtag, Optimus and ATAC. The resulting header looks like the following:

@CO	user command line: STAR --soloType Droplet --soloStrand Forward --runThreadN 8 --genomeDir genome_reference --readFilesIn /cromwell_root/fc-cddd72b5-323c-495c-9557-5057fff0275a/submissions/intermediates/759925b5-00de-45bd-96d9-8384740bd7e9/TestOptimus/743ea945-b6f4-4ca5-9094-186a4a7c8feb/call-Optimus/Optimus/76860243-c175-4024-95bf-9153f8845e50/call-SplitFastq/cacheCopy/glob-ff9a5e75bc9701a883ca32428a133843/fastq_R2_0.fastq.gz /cromwell_root/fc-cddd72b5-323c-495c-9557-5057fff0275a/submissions/intermediates/759925b5-00de-45bd-96d9-8384740bd7e9/TestOptimus/743ea945-b6f4-4ca5-9094-186a4a7c8feb/call-Optimus/Optimus/76860243-c175-4024-95bf-9153f8845e50/call-SplitFastq/cacheCopy/glob-5b3386a102763e9e23988d2e220cbc9d/fastq_R1_0.fastq.gz --readFilesCommand "gunzip -c" --soloCBwhitelist /cromwell_root/gcp-public-data--broad-references/RNA/resources/3M-febrary-2018.txt --soloUMIlen 12 --soloCBlen 16 --soloFeatures Gene --clipAdapterType CellRanger4 --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi --soloUMIdedup 1MM_CR --outSAMtype BAM SortedByCoordinate --outSAMattributes UB UR UY CR CB CY NH GX GN sF cN --soloBarcodeReadLength 0 --soloCellReadStats Standard --soloMultiMappers Uniform --soloUMIfiltering MultiGeneUMI_CR --soloCellFilter EmptyDrops_CR
@CO	Reference genome used: gs://gcp-public-data--broad-references/hg38/v0/star/v2_7_10a/modified_star2.7.10a-Human-GENCODE-build-GRCh38-43.tar

[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':
All WDLs and changelog files appear to be valid for this release.

[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.

[nikellepetrillo]

looks good!

[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':
All WDLs and changelog files appear to be valid for this release.

[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.

[ekiernan]

TestPairedTag, TestOptimus, and TestMultiome all passed in Terra workspace