From eb4454674dc8a3ffe27f2ed756d985c6f3b9a956 Mon Sep 17 00:00:00 2001
From: Lukas Forer <lukas.forer@i-med.ac.at>
Date: Sat, 2 Mar 2024 11:02:05 +0100
Subject: [PATCH] Add contamination status to summary table and commit
 snapshots

---
 reports/report.Rmd             | 21 ++++++++++++--
 tests/mitocalling.nf.test.snap | 50 +++++++++++++++++++++++++++-------
 2 files changed, 58 insertions(+), 13 deletions(-)

diff --git a/reports/report.Rmd b/reports/report.Rmd
index 642ccda..0164a8c 100644
--- a/reports/report.Rmd
+++ b/reports/report.Rmd
@@ -134,11 +134,21 @@ Row
 colors <- c("#28a745", "#dc3545")
 names(colors) <- c("PASSED", "FAILED")
 
+colors_contamination <- c("#dddddd","#28a745", "#dc3545")
+names(colors_contamination) <- c("-", "NO", "YES")
+
 statistics %>%
-  mutate (Sample_Link = link_to_sample(Sample_Label)) %>%
-  select("Sample_Link", "MeanDepth", "CoveragePercentage", "CoveredBases", "MeanBaseQuality", "MeanMapQuality", "qc") %>%
+  mutate (
+    Sample_Link = link_to_sample(Sample_Label),
+    contamination = case_when(
+      qc == "FAILED" ~ "-",
+      Sample_Label %in% contaminated_samples$Sample_Label ~ "YES",
+      TRUE ~ "NO"
+    )
+  ) %>%
+  select("Sample_Link", "MeanDepth", "CoveragePercentage", "CoveredBases", "MeanBaseQuality", "MeanMapQuality", "qc", "contamination") %>%
   datatable(
-    colnames=c("Sample", "Mean Coverage", "Covered Bases (%)", "Covered Bases", "Mean Base Quality", "Mean Mapping Quality", "QC"),
+    colnames=c("Sample", "Mean Coverage", "Covered Bases (%)", "Covered Bases", "Mean Base Quality", "Mean Mapping Quality", "QC", "Cont."),
     options = list(
       bPaginate = FALSE
     ),
@@ -149,6 +159,11 @@ statistics %>%
     'qc',
     backgroundColor = styleEqual(c("PASSED", "FAILED"), colors),
     color = 'white'
+  ) %>% 
+  formatStyle(
+    'contamination',
+    backgroundColor = styleEqual(c("-", "NO", "YES"), colors_contamination),
+    color = 'white'
   )
 ```
 
diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap
index 96415dc..9198b0d 100644
--- a/tests/mitocalling.nf.test.snap
+++ b/tests/mitocalling.nf.test.snap
@@ -9,6 +9,21 @@
         },
         "timestamp": "2024-02-26T23:09:58.251860914"
     },
+    "Runs with 6 samples provided as testdata with mutect2": {
+        "content": [
+            "variants.annotated.txt:md5,efeb591e666bd107fbb0ce47898b6304",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 24,
+                "tasksSucceeded": 24
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T10:54:19.802653"
+    },
     "Runs with single BAM file and mutserve": {
         "content": [
             "variants.annotated.txt:md5,aac0aee87ce1a91f8c35264be248b52e"
@@ -29,34 +44,49 @@
         },
         "timestamp": "2024-02-26T23:03:07.470112898"
     },
-    "Runs with 6 samples provided as testdata": {
+    "Runs with two files and one goes through QC": {
         "content": [
-            "variants.annotated.txt:md5,efeb591e666bd107fbb0ce47898b6304",
+            "variants.annotated.txt:md5,3946a3bd26ceafe8f61903499bfcbb35",
             {
                 "tasksFailed": 0,
-                "tasksCount": 24,
-                "tasksSucceeded": 24
+                "tasksCount": 12,
+                "tasksSucceeded": 12
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-03-01T13:54:57.136897"
+        "timestamp": "2024-02-28T12:32:40.624776"
     },
-    "Runs with two files and one goes through QC": {
+    "Runs with 6 samples provided as testdata with fusion": {
         "content": [
-            "variants.annotated.txt:md5,3946a3bd26ceafe8f61903499bfcbb35",
+            "variants.annotated.txt:md5,b8a0bbf624f5b0ecaac01ca441b50a76",
             {
                 "tasksFailed": 0,
-                "tasksCount": 12,
-                "tasksSucceeded": 12
+                "tasksCount": 40,
+                "tasksSucceeded": 40
             }
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.3"
         },
-        "timestamp": "2024-02-28T12:32:40.624776"
+        "timestamp": "2024-03-02T10:58:52.06124"
+    },
+    "Runs with 6 samples provided as testdata with mutserve": {
+        "content": [
+            "variants.annotated.txt:md5,5c726eaa61eacfb09c64ebaeb9a2a75a",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 25,
+                "tasksSucceeded": 25
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T10:50:44.742545"
     }
 }
\ No newline at end of file