diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ac31dfe..c142eb3 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -77,6 +77,7 @@ jobs: - "phoenix" - "prince" - "rosalind" + - "sage" - "sahmri" - "sanger" - "seg_globe" diff --git a/README.md b/README.md index 1f37d29..d86461c 100644 --- a/README.md +++ b/README.md @@ -10,7 +10,6 @@ A repository for hosting Nextflow configuration files containing custom paramete - [Configuration and parameters](#configuration-and-parameters) - [Offline usage](#offline-usage) - [Adding a new config](#adding-a-new-config) - - [Checking user hostnames](#checking-user-hostnames) - [Testing](#testing) - [Documentation](#documentation) - [Uploading to `nf-core/configs`](#uploading-to-nf-coreconfigs) @@ -131,6 +130,7 @@ Currently documentation is available for the following systems: - [PHOENIX](docs/phoenix.md) - [PRINCE](docs/prince.md) - [ROSALIND](docs/rosalind.md) +- [SAGE BIONETWORKS](docs/sage.md) - [SANGER](docs/sanger.md) - [SEG_GLOBE](docs/seg_globe.md) - [UCT_HPC](docs/uct_hpc.md) diff --git a/conf/sage.config b/conf/sage.config new file mode 100644 index 0000000..e5bfa8b --- /dev/null +++ b/conf/sage.config @@ -0,0 +1,100 @@ +params { + config_profile_description = 'The Sage Bionetworks profile' + config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)' + config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows' +} + +process { + + cpus = { check_max( 1 * slow(task.attempt), 'cpus' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } + time = { check_max( 24.h * task.attempt, 'time' ) } + + errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' } + maxRetries = 5 + maxErrors = '-1' + + // Process-specific resource requirements + withLabel:process_low { + cpus = { check_max( 4 * slow(task.attempt), 'cpus' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } + time = { check_max( 24.h * task.attempt, 'time' ) } + } + withLabel:process_medium { + cpus = { check_max( 12 * slow(task.attempt), 'cpus' ) } + memory = { check_max( 36.GB * task.attempt, 'memory' ) } + time = { check_max( 48.h * task.attempt, 'time' ) } + } + withLabel:process_high { + cpus = { check_max( 24 * slow(task.attempt), 'cpus' ) } + memory = { check_max( 72.GB * task.attempt, 'memory' ) } + time = { check_max( 96.h * task.attempt, 'time' ) } + } + withLabel:process_long { + time = { check_max( 192.h * task.attempt, 'time' ) } + } + withLabel:process_high_memory { + memory = { check_max( 128.GB * task.attempt, 'memory' ) } + } + + // Preventing Sarek labels from using the actual maximums + withLabel:memory_max { + memory = { check_max( 128.GB * task.attempt, 'memory' ) } + } + withLabel:cpus_max { + cpus = { check_max( 24 * slow(task.attempt), 'cpus' ) } + } + +} + +aws { + region = "us-east-1" +} + +params { + igenomes_base = 's3://sage-igenomes/igenomes' + max_memory = 500.GB + max_cpus = 64 + max_time = 168.h // One week +} + +// Function to slow the increase of the resource multipler +// as attempts are made. The rationale is that some CPUs +// don't need to be increased as fast as memory. +def slow(attempt, factor = 2) { + return Math.ceil( attempt / factor) as int +} + + +// Function to ensure that resource requirements don't go +// beyond a maximum limit (copied here for Sarek v2) +def check_max(obj, type) { + if (type == 'memory') { + try { + if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) + return params.max_memory as nextflow.util.MemoryUnit + else + return obj + } catch (all) { + println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'time') { + try { + if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) + return params.max_time as nextflow.util.Duration + else + return obj + } catch (all) { + println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" + return obj + } + } else if (type == 'cpus') { + try { + return Math.min( obj, params.max_cpus as int ) + } catch (all) { + println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" + return obj + } + } +} diff --git a/conf/vsc_ugent.config b/conf/vsc_ugent.config index 9837a54..8fb706b 100644 --- a/conf/vsc_ugent.config +++ b/conf/vsc_ugent.config @@ -20,6 +20,10 @@ singularity { cacheDir = "$scratch_dir/singularity" } +env { + SINGULARITY_CACHEDIR="$scratch_dir/.singularity" +} + // Define profiles for each cluster profiles { skitty { @@ -36,7 +40,6 @@ profiles { executor = 'slurm' queue = 'skitty' maxRetries = 2 - beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity" scratch = "$scratch_dir" } } @@ -55,7 +58,6 @@ profiles { executor = 'slurm' queue = 'swalot' maxRetries = 2 - beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity" scratch = "$scratch_dir" } } @@ -74,7 +76,6 @@ profiles { executor = 'slurm' queue = 'victini' maxRetries = 2 - beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity" scratch = "$scratch_dir" } } @@ -93,7 +94,6 @@ profiles { executor = 'slurm' queue = 'kirlia' maxRetries = 2 - beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity" scratch = "$scratch_dir" } } @@ -112,7 +112,6 @@ profiles { executor = 'slurm' queue = 'doduo' maxRetries = 2 - beforeScript = "export SINGULARITY_CACHEDIR=$scratch_dir/.singularity" scratch = "$scratch_dir" } } diff --git a/docs/sage.md b/docs/sage.md new file mode 100644 index 0000000..133ccec --- /dev/null +++ b/docs/sage.md @@ -0,0 +1,27 @@ +# nf-core/configs: Sage Bionetworks Global Configuration + +To use this custom configuration, run the pipeline with `-profile sage`. This will download and load the [`sage.config`](../conf/sage.config), which contains a number of optimizations relevant to Sage employees running workflows on AWS (_e.g._ using Nextflow Tower). This profile will also load any applicable pipeline-specific configuration. + +This global configuration includes the following tweaks: + +- Update the default value for `igenomes_base` to `s3://sage-igenomes` +- Increase the default time limits because we run pipelines on AWS +- Enable retries by default when exit codes relate to insufficient memory +- Allow pending jobs to finish if the number of retries are exhausted +- Slow the increase in the number of allocated CPU cores on retries +- Define the `check_max()` function, which is missing in Sarek v2 + +## Additional information about iGenomes + +The following iGenomes prefixes have been copied from `s3://ngi-igenomes/` (`eu-west-1`) to `s3://sage-igenomes` (`us-east-1`). See [this script](https://github.com/Sage-Bionetworks-Workflows/nextflow-infra/blob/main/bin/mirror-igenomes.sh) for more information. The `sage-igenomes` S3 bucket has been configured to openly available, but files cannot be downloaded out of `us-east-1` to avoid egress charges. You can check the `conf/igenomes.config` file in each nf-core pipeline to figure out the mapping between genome IDs (_i.e._ for `--genome`) and iGenomes prefixes ([example](https://github.com/nf-core/rnaseq/blob/89bf536ce4faa98b4d50a8ec0a0343780bc62e0a/conf/igenomes.config#L14-L26)). + +- **Human Genome Builds** + - `Homo_sapiens/Ensembl/GRCh37` + - `Homo_sapiens/GATK/GRCh37` + - `Homo_sapiens/UCSC/hg19` + - `Homo_sapiens/GATK/GRCh38` + - `Homo_sapiens/NCBI/GRCh38` + - `Homo_sapiens/UCSC/hg38` +- **Mouse Genome Builds** + - `Mus_musculus/Ensembl/GRCm38` + - `Mus_musculus/UCSC/mm10` diff --git a/nfcore_custom.config b/nfcore_custom.config index 88e7227..4b44d8a 100644 --- a/nfcore_custom.config +++ b/nfcore_custom.config @@ -59,6 +59,7 @@ profiles { phoenix { includeConfig "${params.custom_config_base}/conf/phoenix.config" } prince { includeConfig "${params.custom_config_base}/conf/prince.config" } rosalind { includeConfig "${params.custom_config_base}/conf/rosalind.config" } + sage { includeConfig "${params.custom_config_base}/conf/sage.config" } sahmri { includeConfig "${params.custom_config_base}/conf/sahmri.config" } sanger { includeConfig "${params.custom_config_base}/conf/sanger.config"} seg_globe { includeConfig "${params.custom_config_base}/conf/seg_globe.config"} diff --git a/pipeline/sarek.config b/pipeline/sarek.config index 57d7bdf..512541e 100644 --- a/pipeline/sarek.config +++ b/pipeline/sarek.config @@ -15,4 +15,4 @@ profiles { cfc { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" } cfc_dev { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/cfc.config" } eddie { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/eddie.config" } -} \ No newline at end of file +}