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fix: CLIN-3453 add missing resources for exomiser process in config #51

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merged 1 commit into from
Dec 18, 2024
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fix: CLIN-3453 add missing resources for exomiser process in config #51

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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`
- [#50](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/50) Use container tag 1.20 for splitMultiAllelics process
- [#51](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/51) Add missing ressources for exomiser process in configuration

### `Known issues`
- The nf-core modules that we are using have a potential performance flaw. Typically, the regex used to describe the output files also match the input files (ex: "*.vcf"), which can cause unnecessary file transfers. This has already proven to cause issues on fusion. One fix could be to transfer the whole modules to local to perform the small change necessary to fix this.
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2 changes: 1 addition & 1 deletion modules/local/exomiser/main.nf
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@@ -1,6 +1,6 @@
process EXOMISER {

label 'process_low'
label 'process_medium'

input:
tuple val(meta), path(vcfFile), path(phenoFile), path(analysisFile)
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13 changes: 11 additions & 2 deletions nextflow.config
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Expand Up @@ -58,7 +58,7 @@ params {
//Resources optionsreferenceGenome
//defaults expecting to be overwritten
max_cpus = 16
max_disk = '80.GB'
max_disk = '200.GB'
max_time = '12.h'
max_memory = '120.GB'

Expand Down Expand Up @@ -223,7 +223,8 @@ env {
}

process {
disk = 40.GB
disk = 40.GB

withName: 'variantRecalibratorSNP|variantRecalibratorIndel|applyVQSRIndel|applyVQSRSNP|gatherVCF' {
container = 'broadinstitute/gatk:4.5.0.0'
}
Expand Down Expand Up @@ -295,6 +296,14 @@ process {
disk = { check_max( 80.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'EXOMISER' {
errorStrategy = 'retry'
maxRetries = 2
cpus = { check_max( 6 * task.attempt, 'cpus' ) }
memory = { check_max( 36.GB * task.attempt, 'memory' ) }
disk = { check_max( 150.GB * task.attempt, 'disk' ) }
time = { check_max( 10.h * task.attempt, 'time' ) }
}
withName: 'writemeta' {
container = 'ubuntu:24.10'
}
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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Expand Up @@ -170,7 +170,7 @@
},
"max_disk": {
"type": "string",
"default": "80.GB",
"default": "200.GB",
"description": "Maximum amount of disk space that can be requested for any single job.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"help_text": "Use to set an upper-limit for the disk space requirement for each process. Should be a string in the format integer-unit e.g. `--max_disk '8.GB'`"
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