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Merge pull request #44 from CDCgov/dev
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‎CHANGELOG.md‎

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@@ -13,9 +13,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Added`
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- [PR #44](https://github.com/CDCgov/MIRA-NF/pull/44) - adding configs for other profiles. restore the base config to it's original settings to be used as a template for other config files.
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### `Fixed`
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- [PR #42](https://github.com/CDCgov/MIRA-NF/pull/42) - Fixing how the base base is extracted from the run path for naming parquet and cav files. Will now work with "." in the run name.
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- [PR #43](https://github.com/CDCgov/MIRA-NF/pull/43) - Fixing how the base base is extracted from the run path for naming parquet and cav files. Will now work with "." in the run name.
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### `Dependencies`
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‎DESCRIPTION‎

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Package: mira-nf
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Type: Package
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Title: Nextflow Pipeline for Influenza, SARS-COV-2 and RSV Assembly and Curation
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Version: 1.4.0
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Version: 1.4.1
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Date: 2025-01-23
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Authors@R:
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c(person(given="Ben", family="Rambo-Martin", role=c("led", "aut"),

‎conf/amd.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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mira-nf/mira Nextflow amd config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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A config file for AMD-P. Assumes that all software is installed and available on
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the PATH.
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----------------------------------------------------------------------------------------
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*/
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process {
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cpus = { check_max( 1 * task.attempt, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
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maxRetries = 1
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maxErrors = '-1'
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// Process-specific resource requirements
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withLabel:process_single {
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cpus = { check_max( 1 , 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 6 * task.attempt, 'cpus' ) }
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 16.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 20.h * task.attempt, 'time' ) }
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}
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withLabel:process_high_memory {
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memory = { check_max( 200.GB * task.attempt, 'memory' ) }
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}
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withLabel:error_ignore {
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errorStrategy = 'ignore'
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}
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withLabel:error_retry {
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errorStrategy = 'retry'
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maxRetries = 3
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}
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}

‎conf/aws_mem.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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mira-nf/mira Nextflow local config file
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mira-nf/mira Nextflow aws config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is the config to limit resources in aws environments
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This is the config to limit resources in APHL's aws environments
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----------------------------------------------------------------------------------------
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*/
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‎conf/base.config‎

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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 6 * task.attempt, 'cpus' ) }
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memory = { check_max( 36.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 24.GB * task.attempt, 'memory' ) }
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cpus = { check_max( 12 * task.attempt, 'cpus' ) }
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memory = { check_max( 72.GB * task.attempt, 'memory' ) }
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time = { check_max( 16.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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}
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withLabel:error_retry {
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errorStrategy = 'retry'
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maxRetries = 3
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maxRetries = 2
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}
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}
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}

‎conf/local_base.config‎

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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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mira-nf/mira Nextflow local config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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This is set up like tyhe base config, but with limited resources to run smoothly on a locally
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This is set up like the base config, but with limited resources to run smoothly on a locally
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----------------------------------------------------------------------------------------
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*/
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‎conf/sge_slurm.config‎

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/*
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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mira-nf/mira Nextflow sge and slurm config file
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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A config file, appropriate for general use on most high performance
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compute environments. Assumes that all software is installed and available on
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the PATH.
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----------------------------------------------------------------------------------------
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*/
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process {
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cpus = { check_max( 1 * task.attempt, 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
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maxRetries = 1
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maxErrors = '-1'
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// Process-specific resource requirements
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withLabel:process_single {
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cpus = { check_max( 1 , 'cpus' ) }
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memory = { check_max( 6.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_low {
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cpus = { check_max( 2 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 4.h * task.attempt, 'time' ) }
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}
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withLabel:process_medium {
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cpus = { check_max( 4 * task.attempt, 'cpus' ) }
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memory = { check_max( 12.GB * task.attempt, 'memory' ) }
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time = { check_max( 8.h * task.attempt, 'time' ) }
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}
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withLabel:process_high {
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cpus = { check_max( 8 * task.attempt, 'cpus' ) }
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memory = { check_max( 24.GB * task.attempt, 'memory' ) }
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time = { check_max( 16.h * task.attempt, 'time' ) }
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}
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withLabel:process_long {
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time = { check_max( 20.h * task.attempt, 'time' ) }
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}
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withLabel:process_high_memory {
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memory = { check_max( 200.GB * task.attempt, 'memory' ) }
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}
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withLabel:error_ignore {
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errorStrategy = 'ignore'
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}
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withLabel:error_retry {
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errorStrategy = 'retry'
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maxRetries = 3
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}
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}

‎conf/test_full.config‎

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Defines input files and everything required to run a full size pipeline test.
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Use as follows:
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nextflow run mira/cli -profile test_full,<docker/singularity> --outdir <OUTDIR>
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nextflow run mira-nf/mira -profile test_full,<docker/singularity> --outdir <OUTDIR>
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----------------------------------------------------------------------------------------
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*/

‎nextflow.config‎

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docker.enabled = false
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// Load configs
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includeConfig 'conf/base.config'
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includeConfig 'conf/sge_slurm.config'
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includeConfig 'conf/modules.config'
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executor {
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}
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slurm {
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// Load configs
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includeConfig 'conf/base.config'
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includeConfig 'conf/sge_slurm.config'
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includeConfig 'conf/modules.config'
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process.executor = 'slurm'

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