Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update resource allocations #289

Merged
merged 9 commits into from
May 15, 2024
Merged

update resource allocations #289

merged 9 commits into from
May 15, 2024

Conversation

sorelfitzgibbon
Copy link
Contributor

@sorelfitzgibbon sorelfitzgibbon commented May 13, 2024 •
edited
Loading

Description

Resource allocations updated based on results of 30 PCAWG and 13 SARC (SGSALASC) sarcoma sample runs.
Main changes for F72:

  • convert_BAM2Pileup_SAMtools retry memory substantially increased
  • run_sump_MuSE memory allocation dropped from 80.GB to 18.GB

PCAWG samples described here
SARC samples described here

Sample coverage

dataset type min max average
PCAWG tumor 24x 71x 44x
PCAWG normal 24x 50x 32x
SARC tumor 18x 96x 75x
SARC normal 36x 89x 62.5x

Closes #255 #283

Testing Results

Tested on different PCAWG-63 samples that had failed before this update. They all failed again initially and worked on retry.

main logs:

/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-call-sSNV/sfitz-update-resources_DO220599_ssnv.log
/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-call-sSNV/sfitz-update-resources_DO36881_ssnv.log
/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-call-sSNV/sfitz-update-resources_DO37758_ssnv.log
/hot/code/sfitzgibbon/gitHub/uclahs-cds/pipeline-call-sSNV/sfitz-update-resources_DO38847_ssnv.log

process logs:

/hot/user/sfitzgibbon/PCAWG-63/data/pipeline-runs/sfitz-update-resources-DO220599-ssnv/call-sSNV-8.0.0/SA556937/log-call-sSNV-8.0.0-20240507T214647Z
/hot/user/sfitzgibbon/PCAWG-63/data/pipeline-runs/sfitz-update-resources-DO36881-ssnv/call-sSNV-8.0.0/SA421337/log-call-sSNV-8.0.0-20240507T222604Z
/hot/user/sfitzgibbon/PCAWG-63/data/pipeline-runs/sfitz-update-resources-DO37758-ssnv/call-sSNV-8.0.0/SA433958/log-call-sSNV-8.0.0-20240508T172838Z
/hot/user/sfitzgibbon/PCAWG-63/data/pipeline-runs/sfitz-update-resources-DO38847-ssnv/call-sSNV-8.0.0/SA443714/log-call-sSNV-8.0.0-20240508T181628Z

Testing after updating submodules, nftest

main log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-update-resources/slurm-154972.out
process log: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-update-resources/log-nftest-20240513T232120Z.log

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; I 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.

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","proc_resource_params","call_sIndel_Manta","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","convert_BAM2Pileup_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","create_IndelCandidate_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "24 GB"
+ "16 GB"
@ ["params","proc_resource_params","run_sump_MuSE","retry_strategy","memory","operand"]
- "8 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","2"]
- "9 GB"
+ "11 GB"
@ ["process","withName:call_sIndel_Manta","memory","3"]
- "12 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","closure"]
- "retry_updater(6 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(6 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "5 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "7 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 2 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","2"]
- "16 GB"
+ "28 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(8 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(8 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "24 GB"
+ "16 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(24 GB, add, 8 GB, $task.attempt, memory)"
+ "retry_updater(16 GB, add, 16 GB, $task.attempt, memory)"

test/configtest-F32.json

@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","retry_strategy","memory","operand"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","memory"]
- "16 GB"
+ "12 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "48 GB"
+ "18 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "6 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "9 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","1"]
- "16 GB"
+ "12 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","3"]
- "64 GB"
+ "52 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(16 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(12 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "48 GB"
+ "18 GB"
@ ["process","withName:run_sump_MuSE","memory","2"]
- "64 GB"
+ "34 GB"
@ ["process","withName:run_sump_MuSE","memory","3"]
- "64 GB"
+ "50 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(48 GB, add, 16 GB, $task.attempt, memory)"
+ "retry_updater(18 GB, add, 16 GB, $task.attempt, memory)"

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.

@sorelfitzgibbon
Copy link
Contributor Author

/fix-tests

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with a3a3119. You must review my work before merging this pull request!

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","proc_resource_params","call_sIndel_Manta","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","convert_BAM2Pileup_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","create_IndelCandidate_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "24 GB"
+ "16 GB"
@ ["params","proc_resource_params","run_sump_MuSE","retry_strategy","memory","operand"]
- "8 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","2"]
- "9 GB"
+ "11 GB"
@ ["process","withName:call_sIndel_Manta","memory","3"]
- "12 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","closure"]
- "retry_updater(6 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(6 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "5 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "7 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 2 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","2"]
- "16 GB"
+ "28 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(8 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(8 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "24 GB"
+ "16 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(24 GB, add, 8 GB, $task.attempt, memory)"
+ "retry_updater(16 GB, add, 16 GB, $task.attempt, memory)"

test/configtest-F32.json

@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","retry_strategy","memory","operand"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","memory"]
- "16 GB"
+ "12 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "48 GB"
+ "18 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "6 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "9 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","1"]
- "16 GB"
+ "12 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","3"]
- "64 GB"
+ "52 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(16 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(12 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "48 GB"
+ "18 GB"
@ ["process","withName:run_sump_MuSE","memory","2"]
- "64 GB"
+ "34 GB"
@ ["process","withName:run_sump_MuSE","memory","3"]
- "64 GB"
+ "50 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(48 GB, add, 16 GB, $task.attempt, memory)"
+ "retry_updater(18 GB, add, 16 GB, $task.attempt, memory)"

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.

@sorelfitzgibbon
Copy link
Contributor Author

/fix-tests

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with d63aa1b. You must review my work before merging this pull request!

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

Alas, some of the Nextflow configuration tests failed!

test/configtest-F16.json

@ ["params","proc_resource_params","call_sIndel_Manta","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","convert_BAM2Pileup_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","create_IndelCandidate_SAMtools","retry_strategy","memory","operand"]
- "3 GB"
+ "5 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "24 GB"
+ "16 GB"
@ ["params","proc_resource_params","run_sump_MuSE","retry_strategy","memory","operand"]
- "8 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","2"]
- "9 GB"
+ "11 GB"
@ ["process","withName:call_sIndel_Manta","memory","3"]
- "12 GB"
+ "16 GB"
@ ["process","withName:call_sIndel_Manta","memory","closure"]
- "retry_updater(6 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(6 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "5 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "7 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 2 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:convert_BAM2Pileup_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","2"]
- "4 GB"
+ "6 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","3"]
- "7 GB"
+ "11 GB"
@ ["process","withName:create_IndelCandidate_SAMtools","memory","closure"]
- "retry_updater(1 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(1 GB, add, 5 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","2"]
- "16 GB"
+ "28 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(8 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(8 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "24 GB"
+ "16 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(24 GB, add, 8 GB, $task.attempt, memory)"
+ "retry_updater(16 GB, add, 16 GB, $task.attempt, memory)"

test/configtest-F32.json

@ ["params","proc_resource_params","call_sSNV_Mutect2","memory"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","call_sSNV_Mutect2","retry_strategy","memory","operand"]
- "3 GB"
+ "2 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","memory"]
- "16 GB"
+ "12 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","operand"]
- "2"
+ "20 GB"
@ ["params","proc_resource_params","run_LearnReadOrientationModel_GATK","retry_strategy","memory","strategy"]
- "exponential"
+ "add"
@ ["params","proc_resource_params","run_sump_MuSE","memory"]
- "48 GB"
+ "18 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","1"]
- "3 GB"
+ "2 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","2"]
- "6 GB"
+ "4 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","3"]
- "9 GB"
+ "6 GB"
@ ["process","withName:call_sSNV_Mutect2","memory","closure"]
- "retry_updater(3 GB, add, 3 GB, $task.attempt, memory)"
+ "retry_updater(2 GB, add, 2 GB, $task.attempt, memory)"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","1"]
- "16 GB"
+ "12 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","3"]
- "64 GB"
+ "52 GB"
@ ["process","withName:run_LearnReadOrientationModel_GATK","memory","closure"]
- "retry_updater(16 GB, exponential, 2, $task.attempt, memory)"
+ "retry_updater(12 GB, add, 20 GB, $task.attempt, memory)"
@ ["process","withName:run_sump_MuSE","memory","1"]
- "48 GB"
+ "18 GB"
@ ["process","withName:run_sump_MuSE","memory","2"]
- "64 GB"
+ "34 GB"
@ ["process","withName:run_sump_MuSE","memory","3"]
- "64 GB"
+ "50 GB"
@ ["process","withName:run_sump_MuSE","memory","closure"]
- "retry_updater(48 GB, add, 16 GB, $task.attempt, memory)"
+ "retry_updater(18 GB, add, 16 GB, $task.attempt, memory)"

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.

@sorelfitzgibbon
Copy link
Contributor Author

/fix-tests

@github-actions GitHub Actions
Copy link

Bleep bloop, I am a robot.

I have updated all of the failing tests for you with 6e2cbeb. You must review my work before merging this pull request!

@sorelfitzgibbon
Copy link
Contributor Author

@yashpatel6 this is ready for review

yashpatel6
yashpatel6 reviewed May 14, 2024
View reviewed changes
Copy link
Contributor

@yashpatel6 yashpatel6 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Generally no concerns, a couple of comments:

CHANGELOG.md Outdated Show resolved Hide resolved
config/F32.config Show resolved Hide resolved
config/F32.config Show resolved Hide resolved
@sorelfitzgibbon @yashpatel6
Update CHANGELOG.md
1c02893 
Co-authored-by: Yash Patel <[email protected]>
yashpatel6
yashpatel6 approved these changes May 15, 2024
View reviewed changes
Copy link
Contributor

@yashpatel6 yashpatel6 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good!

@sorelfitzgibbon sorelfitzgibbon merged commit e038942 into main May 15, 2024
7 checks passed
@sorelfitzgibbon sorelfitzgibbon deleted the sfitz-update-resources branch May 15, 2024 17:33
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@yashpatel6 yashpatel6 yashpatel6 approved these changes

@tyamaguchi-ucla tyamaguchi-ucla Awaiting requested review from tyamaguchi-ucla tyamaguchi-ucla is a code owner

@maotian06 maotian06 Awaiting requested review from maotian06 maotian06 is a code owner

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

Running out of memory in 'somaticsniper:convert_BAM2Pileup_SAMtools (2)'
2 participants
@sorelfitzgibbon @yashpatel6