diff --git a/NextflowModules b/NextflowModules index a100d99..003689f 160000 --- a/NextflowModules +++ b/NextflowModules @@ -1 +1 @@ -Subproject commit a100d9934638f11f68004859368bfdf36734066c +Subproject commit 003689f7f12fbca246a98049eae2c978c387c15a diff --git a/WES.config b/WES.config index e91920e..578bd11 100644 --- a/WES.config +++ b/WES.config @@ -328,6 +328,17 @@ process { mode = 'copy' } } + + withLabel: Workflow_Export_Params { + cpus = 2 + memory = '5G' + time = '10m' + + publishDir { + path = "$params.outdir/log" + mode = 'copy' + } + } } report { @@ -371,7 +382,7 @@ profiles { queueStatInterval = '5min' submitRatelimit = '10sec' } - + mail { smtp.host = 'localhost' } diff --git a/WES.nf b/WES.nf index fcd9a84..753afbb 100644 --- a/WES.nf +++ b/WES.nf @@ -3,6 +3,7 @@ nextflow.preview.dsl=2 // Utils modules include extractFastqPairFromDir from './NextflowModules/Utils/fastq.nf' +include ExportParams as Workflow_ExportParams from './NextflowModules/Utils/workflow.nf' // Mapping modules include BWAMapping from './NextflowModules/BWA-Mapping/bwa-0.7.17_samtools-1.9/Mapping.nf' params( @@ -161,8 +162,9 @@ workflow { //SavePedFile SavePedFile() - // Repository versions + // Create log files: Repository versions and Workflow params VersionLog() + Workflow_ExportParams() } // Workflow completion notification diff --git a/WES_Fingerprint.nf b/WES_Fingerprint.nf index a62f50c..7ec762b 100644 --- a/WES_Fingerprint.nf +++ b/WES_Fingerprint.nf @@ -1,7 +1,9 @@ #!/usr/bin/env nextflow nextflow.preview.dsl=2 +// Utils modules include extractBamFromDir from './NextflowModules/Utils/bam.nf' +include ExportParams as Workflow_ExportParams from './NextflowModules/Utils/workflow.nf' // Fingerprint modules include UnifiedGenotyper as GATK_UnifiedGenotyper from './NextflowModules/GATK/3.8-1-0-gf15c1c3ef/UnifiedGenotyper.nf' params(gatk_path: "$params.gatk_path", genome:"$params.genome", optional: "--intervals $params.dxtracks_path/$params.fingerprint_target --output_mode EMIT_ALL_SITES") @@ -10,8 +12,11 @@ def bam_files = extractBamFromDir(params.bam_path) def analysis_id = params.outdir.split('/')[-1] workflow { - // GATK UnifiedGenotyper (fingerprint) GATK_UnifiedGenotyper(bam_files) + + // Create log files: Repository versions and Workflow params + VersionLog() + Workflow_ExportParams() } // Workflow completion notification @@ -40,6 +45,7 @@ process VersionLog { tag {"VersionLog ${analysis_id}"} label 'VersionLog' shell = ['/bin/bash', '-eo', 'pipefail'] + cache = false //Disable cache to force a new version log when restarting the workflow. output: path('repository_version.log')