From 90295269987be6cc9d43f1178242261b08797cab Mon Sep 17 00:00:00 2001 From: Mark Schreiber Date: Fri, 5 Nov 2021 12:17:55 -0400 Subject: [PATCH 1/2] add information about example inputs and runtimes --- .../gatk-best-practices-project/README.md | 29 +++++++++++++++++-- examples/nf-core-project/README.md | 20 ++++++++++++- 2 files changed, 45 insertions(+), 4 deletions(-) diff --git a/examples/gatk-best-practices-project/README.md b/examples/gatk-best-practices-project/README.md index be369e1a..7c2258d8 100644 --- a/examples/gatk-best-practices-project/README.md +++ b/examples/gatk-best-practices-project/README.md @@ -1,3 +1,26 @@ -This project includes workflows based on [GATK Best Practices](https://gatk.broadinstitute.org/hc/en-us), developed by -the [Broad Institute](https://www.broadinstitute.org/). More information on how these workflows work is available in -the [GATK Workflows Github repository](/~https://github.com/gatk-workflows). \ No newline at end of file +## Introduction + +This project includes workflows based on [GATK Best Practices](https://gatk.broadinstitute.org/hc/en-us), developed by +the [Broad Institute](https://www.broadinstitute.org/). More information on how these workflows work is available in +the [GATK Workflows Github repository](/~https://github.com/gatk-workflows). + +## Example Workflow Runtimes + +These "wall" times were recorded using the project's `spotCtx` context in `us-east-1` with a maximum of 256 vCPUs. Times include the time from workflow submission +to completion and include any time needed for the AWS Batch service to provision compute (cold start time). +The results indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries +of tasks due to network errors or spot instance interruptions. No call caching was used when producing these timings. + +The inputs used to run the workflows are those specified in the `inputs.json` files of their respective workflows + +| Workflow | Runtime (minutes) | +| -------- | ----------------- | +| seq-format-validation | 19 | +| paired-fastq-to-unmapped-bam | 12 | +| interleaved-fastq-to-paired-fastq | 4 | +| cram-to-bam | 18 | +| bam-to-unmapped-bams | 15 | +| gatk4-data-processing | 32 | +| gatk4-germline-snps-indels | 29 | +| gatk4-rnaseq-germline-snps-indels | 236 | +| gatk4-basic-joint-genotyping | 189 | diff --git a/examples/nf-core-project/README.md b/examples/nf-core-project/README.md index 63e17816..5b9a9b63 100644 --- a/examples/nf-core-project/README.md +++ b/examples/nf-core-project/README.md @@ -1,6 +1,24 @@ +## Introduction + This project uses workflows from the [nf-core](https://nf-co.re/) repository. For licensing terms, credits and citation of individual workflows please refer to the following links: * /~https://github.com/nf-core/rnaseq * /~https://github.com/nf-core/sarek -* /~https://github.com/nf-core/atacseq \ No newline at end of file +* /~https://github.com/nf-core/atacseq + +## Example Workflow Runtimes + +These times were recorded using the project's `bigMemCtx` context in `us-east-1` with a maximum of 256 vCPUs. Times include the time from workflow submission +to completion and for the AWS Batch service to provision compute resources (cold start time). Not included is the time required for the Nextflow headnode startup. +The results indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries +of tasks due to task failures. Caching of tasks was not used in this evaluation. + +Workflow inputs were those defined in the respective `*inputs.json` files + + +| Workflow | Runtime (minutes) | +| -------- | ----------------- | +| atacseq | 139 | +| rnaseq | 458 | +| sarek | 359 | \ No newline at end of file From ae573293bfeaade9a13d070ec3c0c15afd9e1f7a Mon Sep 17 00:00:00 2001 From: Mark Schreiber Date: Fri, 5 Nov 2021 15:05:16 -0400 Subject: [PATCH 2/2] fixed typo --- examples/gatk-best-practices-project/README.md | 2 +- examples/nf-core-project/README.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/gatk-best-practices-project/README.md b/examples/gatk-best-practices-project/README.md index 7c2258d8..19f433dd 100644 --- a/examples/gatk-best-practices-project/README.md +++ b/examples/gatk-best-practices-project/README.md @@ -8,7 +8,7 @@ the [GATK Workflows Github repository](/~https://github.com/gatk-workflows). These "wall" times were recorded using the project's `spotCtx` context in `us-east-1` with a maximum of 256 vCPUs. Times include the time from workflow submission to completion and include any time needed for the AWS Batch service to provision compute (cold start time). -The results indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries +The results are indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries of tasks due to network errors or spot instance interruptions. No call caching was used when producing these timings. The inputs used to run the workflows are those specified in the `inputs.json` files of their respective workflows diff --git a/examples/nf-core-project/README.md b/examples/nf-core-project/README.md index 5b9a9b63..78f83344 100644 --- a/examples/nf-core-project/README.md +++ b/examples/nf-core-project/README.md @@ -11,7 +11,7 @@ workflows please refer to the following links: These times were recorded using the project's `bigMemCtx` context in `us-east-1` with a maximum of 256 vCPUs. Times include the time from workflow submission to completion and for the AWS Batch service to provision compute resources (cold start time). Not included is the time required for the Nextflow headnode startup. -The results indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries +The results are indicative only and runtimes will vary based on the resources allocated by AWS Batch as well as any automated retries of tasks due to task failures. Caching of tasks was not used in this evaluation. Workflow inputs were those defined in the respective `*inputs.json` files