diff --git a/README.md b/README.md index 0d561fc..d86461c 100644 --- a/README.md +++ b/README.md @@ -202,7 +202,6 @@ Currently documentation is available for the following pipelines within specific - [MUNIN](docs/pipeline/rnavar/munin.md) - sarek - [MUNIN](docs/pipeline/sarek/munin.md) - - [SAGE BIONETWORKS](docs/pipeline/sarek/sage.md) - [UPPMAX](docs/pipeline/sarek/uppmax.md) - taxprofiler - [EVA](docs/pipeline/taxprofiler/eva.md) diff --git a/conf/pipeline/sarek/sage.config b/conf/pipeline/sarek/sage.config deleted file mode 100644 index b7766bc..0000000 --- a/conf/pipeline/sarek/sage.config +++ /dev/null @@ -1,37 +0,0 @@ -params { - config_profile_description = 'The Sage Bionetworks profile' - config_profile_contact = 'Bruno Grande (@BrunoGrandePhD)' - config_profile_url = 'https://github.com/Sage-Bionetworks-Workflows' -} - -// Function to ensure that resource requirements don't go beyond a maximum limit -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: $obj" - return obj - } - } -} diff --git a/conf/sage.config b/conf/sage.config index b559f79..e5bfa8b 100644 --- a/conf/sage.config +++ b/conf/sage.config @@ -67,7 +67,7 @@ def slow(attempt, factor = 2) { // Function to ensure that resource requirements don't go -// beyond a maximum limit +// beyond a maximum limit (copied here for Sarek v2) def check_max(obj, type) { if (type == 'memory') { try { diff --git a/docs/pipeline/sarek/sage.md b/docs/pipeline/sarek/sage.md deleted file mode 100644 index 646fdda..0000000 --- a/docs/pipeline/sarek/sage.md +++ /dev/null @@ -1,7 +0,0 @@ -# nf-core/configs: Sage Bionetworks Sarek-Specific Configuration - -To use this custom configuration, run the pipeline with `-profile sage`. This will download and load the [`sage.config`](../conf/sage.config), which contains a number of optimizations relevant to Sage employees running workflows on AWS (_e.g._ using Nextflow Tower). This profile will also load any applicable pipeline-specific configuration. - -In addition to the global configuration described [here](../../sage.md), this Sarek-specific configuration includes the following tweaks: - -- Define the `check_max()` function, which is missing in Sarek v2. diff --git a/docs/sage.md b/docs/sage.md index 5b0fa49..133ccec 100644 --- a/docs/sage.md +++ b/docs/sage.md @@ -9,6 +9,7 @@ This global configuration includes the following tweaks: - Enable retries by default when exit codes relate to insufficient memory - Allow pending jobs to finish if the number of retries are exhausted - Slow the increase in the number of allocated CPU cores on retries +- Define the `check_max()` function, which is missing in Sarek v2 ## Additional information about iGenomes diff --git a/pipeline/sarek.config b/pipeline/sarek.config index 36efc99..512541e 100644 --- a/pipeline/sarek.config +++ b/pipeline/sarek.config @@ -15,5 +15,4 @@ profiles { cfc { includeConfig "${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" } - sage { includeConfig "${params.custom_config_base}/conf/pipeline/sarek/sage.config" } }