Fix linting problems

.nf-core.yml

@@ -1 +1,9 @@
 repository_type: pipeline
+lint:
+  template_strings:
+  - modules/local/report/create/app/templates/tf.html
+  - modules/local/report/create/app/templates/tg.html
+  - modules/local/report/create/app/templates/macros.html
+  - modules/local/report/create/app/templates/configuration.html
+  - modules/local/report/create/app/templates/snp.html
+  - modules/local/report/create/app/templates/base.html

modules/local/report/create/main.nf

@@ -18,7 +18,8 @@ process CREATE {
     path(schema)
 
     output:
-    path("report")
+    path("report")      , emit: report
+    path("versions.yml"), emit: versions
 
     script:
     params_string = JsonOutput.toJson(params)

modules/local/report/create/templates/build.py

@@ -1,10 +1,12 @@
 #!/usr/bin/env python3
 
 from jinja2 import Environment, PackageLoader, select_autoescape
+import jinja2
 import os
 import shutil
 import json
 import pandas as pd
+import sys
 from collections import defaultdict
 
 module_app = os.path.abspath("$moduleDir/app")
@@ -121,3 +123,9 @@
 
 with open(os.path.join(out_dir, "ranking.js"), "w") as f:
     f.write(ranking_js.render())
+
+with open("versions.yml", "w") as f:
+    f.write('"${task.process}":\\n')
+    f.write(f'  python: "{sys.executable}"\\n')
+    f.write(f'  pandas: "{pd.__version__}"\\n')
+    f.write(f'  jinja2: "{jinja2.__version__}"\\n')

subworkflows/local/ranking.nf

@@ -51,7 +51,7 @@ workflow RANKING {
                                     COMBINE_TFS_PER_ASSAY.out.versions,
                                     COMBINE_TFS_ACROSS_ASSAYS.out.versions,
                                     COMBINE_TGS_PER_ASSAY.out.versions,
-                                    COMBINE_TGS_PER_ASSAY.out.versions
+                                    COMBINE_TGS_ACROSS_ASSAYS.out.versions
     )
 
 

subworkflows/local/report.nf

@@ -7,6 +7,8 @@ workflow REPORT {
     ch_differential
 
     main:
+    ch_versions = Channel.empty()
+
     CREATE(ch_tf_ranking.map{meta, ranking -> ranking}
                             .collect()
                             .map{rankings -> [[id: "tfs"], rankings]},
@@ -17,4 +19,9 @@ workflow REPORT {
                             .collect()
                             .map{diffs -> [[id: "diffs"], diffs]},
             params, Channel.value(file(projectDir + "/nextflow_schema.json")))
+
+    ch_versions = ch_versions.mix(CREATE.out.versions)
+
+    emit:
+    versions = ch_versions
 }

workflows/tfactivity.nf

@@ -110,18 +110,20 @@ workflow TFACTIVITY {
         alpha
     )
 
-    ch_versions = ch_versions.mix(
-        COUNTS.out.versions,
-        PEAKS.out.versions,
-        DYNAMITE.out.versions
-    )
-
     REPORT(
         RANKING.out.tf_ranking,
         RANKING.out.tg_ranking,
         COUNTS.out.differential
     )
 
+    ch_versions = ch_versions.mix(
+        COUNTS.out.versions,
+        PEAKS.out.versions,
+        DYNAMITE.out.versions,
+        RANKING.out.versions,
+        REPORT.out.versions
+    )
+
     //
     // Collate and save software versions
     //