diff --git a/examples/gatk-best-practices-project/README.md b/examples/gatk-best-practices-project/README.md index be369e1a..19f433dd 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 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 + +| 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..78f83344 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 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 + + +| Workflow | Runtime (minutes) | +| -------- | ----------------- | +| atacseq | 139 | +| rnaseq | 458 | +| sarek | 359 | \ No newline at end of file