Add in index file for azure

[vsmalladi]

Description

Added an index file for alignment of bam file so that it is used for the next step. Azure needs explicit path for the index file

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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?

[dsde-jenkins]

Can one of the admins verify this patch?

[dsde-jenkins]

Can one of the admins verify this patch?

[jessicaway]

Hi @vsmalladi,

The code you have added looks ok, except that the AlignPairedEnd task does not currently output a bam index file. (see code here)

Can you help me understand what the index file is needed for? For this to work, we will also need to change the AlignPairedEnd task to generate and output a bam index file.

[jessicaway]

test this please (this is to trigger the CI/CD to run the tests)