Collect nextflow session and run ids (#10)

* Collect nextflow session and run ids

* bump version

main.nf

@@ -22,11 +22,15 @@ include { collect_provenance }         from './modules/provenance.nf'
 
 
 workflow {
-    ch_start_time = Channel.of(LocalDateTime.now())
-    ch_pipeline_name = Channel.of(workflow.manifest.name)
-    ch_pipeline_version = Channel.of(workflow.manifest.version)
-
-    ch_pipeline_provenance = pipeline_provenance(ch_pipeline_name.combine(ch_pipeline_version).combine(ch_start_time))
+    ch_workflow_metadata = Channel.value([
+	workflow.sessionId,
+	workflow.runName,
+	workflow.manifest.name,
+	workflow.manifest.version,
+	workflow.start,
+    ])
+
+    ch_pipeline_provenance = pipeline_provenance(ch_workflow_metadata)
 
     if (params.samplesheet_input != 'NO_FILE') {
 	ch_fastq = Channel.fromPath(params.samplesheet_input).splitCsv(header: true).map{ it -> [it['ID'], [it['R1'], it['R2'], it['LONG']]] }

modules/provenance.nf

@@ -20,20 +20,22 @@ process collect_provenance {
 
 process pipeline_provenance {
 
-  tag { pipeline_name + " / " + pipeline_version }
+    tag { pipeline_name + " / " + pipeline_version }
 
-  executor 'local'
+    executor 'local'
 
-  input:
-  tuple val(pipeline_name), val(pipeline_version), val(analysis_start)
+    input:
+    tuple val(session_id), val(run_name), val(pipeline_name), val(pipeline_version), val(analysis_start)
 
-  output:
-  file("pipeline_provenance.yml")
+    output:
+    file("pipeline_provenance.yml")
 
-  script:
-  """
-  printf -- "- pipeline_name: ${pipeline_name}\\n"             >> pipeline_provenance.yml
-  printf -- "  pipeline_version: ${pipeline_version}\\n"       >> pipeline_provenance.yml
-  printf -- "  timestamp_analysis_start: ${analysis_start}\\n" >> pipeline_provenance.yml
-  """
+    script:
+    """
+    printf -- "- pipeline_name: ${pipeline_name}\\n"             >> pipeline_provenance.yml
+    printf -- "  pipeline_version: ${pipeline_version}\\n"       >> pipeline_provenance.yml
+    printf -- "  nextflow_session_id: ${session_id}\\n"          >> pipeline_provenance.yml
+    printf -- "  nextflow_run_name: ${run_name}\\n"              >> pipeline_provenance.yml
+    printf -- "  timestamp_analysis_start: ${analysis_start}\\n" >> pipeline_provenance.yml
+    """
 }

nextflow.config

@@ -1,7 +1,7 @@
 manifest {
     author = 'Dan Fornika'
     name = 'BCCDC-PHL/plasmid-assembly'
-    version = '0.1.1'
+    version = '0.1.2'
     description = 'Nextflow pipeline for plasmid assembly'
     mainScript = 'main.nf'
     nextflowVersion = '>=20.01.0'