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Code Issues Releases Packages Activity

Try to reduce MALT memory

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James Fellows Yates 2022-11-24 15:51:12 +01:00
parent 131b39aa8b
commit a20b3e3c58
5 changed files with 12 additions and 7 deletions
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1
conf/test.config
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@ -51,6 +51,7 @@ params {
process { process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
ext.args = "-m ${params.malt_mode} -J-Xmx8G"
} }
withName: MEGAN_RMA2INFO_TSV { withName: MEGAN_RMA2INFO_TSV {
maxForks = 1 maxForks = 1

1
conf/test_nopreprocessing.config
View file

@ -45,5 +45,6 @@ params {
process { process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
ext.args = "-m ${params.malt_mode} -J-Xmx8G"
} }
} }

1
conf/test_nothing.config
View file

@ -44,5 +44,6 @@ params {
process { process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
ext.args = "-m ${params.malt_mode} -J-Xmx8G"
} }
} }

1
conf/test_pep.config
View file

@ -37,6 +37,7 @@ params {
process { process {
withName: MALT_RUN { withName: MALT_RUN {
maxForks = 1 maxForks = 1
ext.args = "-m ${params.malt_mode} -J-Xmx8G"
} }
withName: MEGAN_RMA2INFO { withName: MEGAN_RMA2INFO {
maxForks = 1 maxForks = 1

15
lib/WorkflowMain.groovy
View file

@ -12,9 +12,9 @@ class WorkflowMain {
// TODO nf-core: Add Zenodo DOI for pipeline after first release // TODO nf-core: Add Zenodo DOI for pipeline after first release
//"* The pipeline\n" + //"* The pipeline\n" +
//" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
"* The nf-core framework\n" + '* The nf-core framework\n' +
" https://doi.org/10.1038/s41587-020-0439-x\n\n" + ' https://doi.org/10.1038/s41587-020-0439-x\n\n' +
"* Software dependencies\n" + '* Software dependencies\n' +
" https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
} }
@ -53,15 +53,15 @@ class WorkflowMain {
System.exit(0) System.exit(0)
} }
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Validate workflow parameters via the JSON schema // Validate workflow parameters via the JSON schema
if (params.validate_params) { if (params.validate_params) {
NfcoreSchema.validateParameters(workflow, params, log) NfcoreSchema.validateParameters(workflow, params, log)
} }
// Print parameter summary log to screen
log.info paramsSummaryLog(workflow, params, log)
// Check that a -profile or Nextflow config has been provided to run the pipeline // Check that a -profile or Nextflow config has been provided to run the pipeline
NfcoreTemplate.checkConfigProvided(workflow, log) NfcoreTemplate.checkConfigProvided(workflow, log)
@ -90,4 +90,5 @@ class WorkflowMain {
} }
return null return null
} }
} }