Optimize Manta CPU

[Faizal-Eeman]

Description

Increment CPU allocation for Manta.

The increments in this PR were primarily adapted from pipeline-call-sSNV and tailored to pipeline-call-gSV's requirements.

Closes #154

Testing Results

Node	Sample	BAM Size	Old Runtime (CPU = 1)	New Runtime (CPU = n)
F16	HG003-5X	21G	1h 27m	11m 38s
F32	ILHNLNEV000002-N001-B01-F	85GB	7h 38m	34m
F72	ZMBNGIAB000008-N001-A01-F	369GB	>20h still running	6h 1m

output dir: /hot/software/pipeline/pipeline-call-gSV/Nextflow/development/unreleased/mmootor-optimize-manta-cpu/

Checklist

• I have read the code review guidelines and the code review best practice on GitHub check-list.

• I have reviewed the Nextflow pipeline standards.

• The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].

• I have set up or verified the branch protection rule following the github standards before opening this pull request.

• I have added my name to the contributors listings in the manifest block in the nextflow.config as part of this pull request, am listed
  already, or do not wish to be listed. (This acknowledgement is optional.)

• I have added the changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.

• I have updated the version number in the metadata.yaml and manifest block of the nextflow.config file following semver, or the version number has already been updated. (Leave it unchecked if you are unsure about new version number and discuss it with the infrastructure team in this PR.)

• I have tested the pipeline on at least one A-mini sample with run_delly = true, run_manta = true, run_qc = true. For run_delly = true, I have tested 'variant_type' set to gSV, gCNV, and both. The paths to the test config files and output directories are captured above in the Testing Results section.

[github-actions]

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","proc_resource_params","call_gSV_Manta","cpus"]
- "1"
+ "6"
@ ["process","withName:call_gSV_Manta","cpus"]
- "1"
+ "6"

If the above changes are surprising, stop and determine what happened.

If the above changes are expected, there are two ways to fix this:

1. Automatically: Post a comment starting with "/fix-tests" (without the quotes) and I will update the tests for you (you must review my work afterwards).
2. Manually: Follow these steps on Confluence.

[yashpatel6]

/fix-tests

[yashpatel6]

Any reason to only update the F16 and F32 configs and not the rest?

[github-actions]

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with 4b7584b. You must review my work before merging this pull request!

[Faizal-Eeman]

Any reason to only update the F16 and F32 configs and not the rest?

@yashpatel6

• F72 test was in progress at the time of opening the PR. It's done now.
• Updating M64 as well but without a test.
• F2 update wouldn't matter as Manta doesn't run on F2.

[yashpatel6]

Looks good!

[tyamaguchi-ucla]

(question: non-blocking) @Faizal-Eeman can you remind us of the optimal #CPU based on the existing benchmarking?

[Faizal-Eeman]

Based on the paper you shared (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10976732/figure/Fig4/), it seems like higher the CPU better is the runtime for Manta. So I set 30 CPUs, so that we still have enough CPUs left to allot to Delly (& other callers) in the future.