Merge pull request #5 from phac-nml/update-json

Adds Program Outputs to Irida Next JSON Output File
phac-nml · Dec 13, 2024 · 8c43747 · 8c43747
2 parents 484c1b6 + 6b3fa13
commit 8c43747
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 0 deletions.
diff --git a/conf/iridanext.config b/conf/iridanext.config
@@ -13,6 +13,8 @@ iridanext {
                 "**/distances/profile_dists.results.text",
                 "**/distances/profile_dists.run.json",
                 "**/merged/locidex.merge.profile.tsv",
+                "**/process/results.tsv",
+                "**/process/results.xlsx"
             ]
         }
     }

diff --git a/tests/pipelines/main.nf.test b/tests/pipelines/main.nf.test
@@ -87,6 +87,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()
@@ -226,6 +228,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()
@@ -273,6 +277,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()
@@ -334,6 +340,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()
@@ -392,6 +400,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()
@@ -444,6 +454,8 @@ nextflow_pipeline {
             assert iridanext_global.findAll { it.path == "distances/profile_dists.query_profile.text" }.size() == 1
             assert iridanext_global.findAll { it.path == "distances/profile_dists.allele_map.json" }.size() == 1
             assert iridanext_global.findAll { it.path == "merged/locidex.merge.profile.tsv" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.xlsx" }.size() == 1
+            assert iridanext_global.findAll { it.path == "process/results.tsv" }.size() == 1
 
             assert iridanext_samples.isEmpty()
             assert iridanext_metadata.isEmpty()