Add params export function

UMCUGenetics · Nov 15, 2021 · 43b4d4b · 43b4d4b
1 parent e933ad0
commit 43b4d4b
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Showing 4 changed files with 23 additions and 4 deletions.
diff --git a/NextflowModules b/NextflowModules
diff --git 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
@@ -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
@@ -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')