Merge branch 'add-params-table' into 'dev'

Add params table in report and process

See merge request epi2melabs/workflow-containers/wf-template!20

bin/report.py

@@ -16,6 +16,9 @@ def main():
     parser.add_argument(
         "--versions", required=True,
         help="directory containing CSVs containing name,version.")
+    parser.add_argument(
+        "--params", default=None, required=True,
+        help="A JSON file containing the workflow parameter key/values")
     parser.add_argument(
         "--revision", default='unknown',
         help="git branch/tag of the executed workflow")
@@ -32,6 +35,8 @@ def main():
         section=fastcat.full_report(args.summaries))
     report.add_section(
         section=scomponents.version_table(args.versions))
+    report.add_section(
+        section=scomponents.params_table(args.params))
 
     # write report
     report.write(args.report)

main.nf

@@ -10,6 +10,7 @@
 //   iii) a second concreate, but anonymous, workflow scope to be used
 //        as an entry point when using this workflow in isolation.
 
+import groovy.json.JsonBuilder
 nextflow.enable.dsl = 2
 
 include { fastq_ingress } from './lib/fastqingress' 
@@ -58,15 +59,29 @@ process getVersions {
     """
 }
 
+process getParams {
+    label "pysam"
+    cpus 1
+    output:
+        path "params.json"
+    script:
+        def paramsJSON = new JsonBuilder(params).toPrettyString()
+    """
+    # Output nextflow params object to JSON
+    echo '$paramsJSON' > params.json
+    """
+}
+
 process makeReport {
     label "pysam"
     input:
         path "seqs.txt"
         path "versions/*"
+        path "params.json"
     output:
         path "wf-template-report.html"
     """
-    report.py wf-template-report.html --versions versions seqs.txt
+    report.py wf-template-report.html --versions versions seqs.txt --params params.json
     """
 }
 
@@ -95,7 +110,8 @@ workflow pipeline {
     main:
         summary = summariseReads(reads)
         software_versions = getVersions()
-        report = makeReport(summary, software_versions.collect())
+        workflow_params = getParams()
+        report = makeReport(summary, software_versions.collect(), workflow_params)
     emit:
         summary.concat(report)
 }