Fix issue with multiple contigs in coverage report

modules/local/quality_control.nf

@@ -1,6 +1,6 @@
 process QUALITY_CONTROL {
 
-    publishDir "${params.output_reports}", mode: "copy", pattern: '*.html'
+    publishDir "${params.output_reports}/multiqc", mode: "copy", pattern: '*.html'
 
     input:
     path excluded_samples
@@ -10,6 +10,6 @@ process QUALITY_CONTROL {
 	path "*.html"
 
 	"""
-	multiqc . 
+	multiqc . --filename index.html
 	"""
 }

modules/local/sample_report.nf

@@ -27,10 +27,18 @@ process SAMPLE_REPORT {
     echo -e "Base Quality\t${params.baseQ}" >> params.txt
     echo -e "Map Quality\t${params.mapQ}" >> params.txt
     echo -e "Alignment Quality\t${params.alignQ}" >> params.txt  
+    echo -e "Mutserv\t\${MUTSERV_VERSION}" >> params.txt 
+    echo -e "Haplocheck\t\${HAPLOCHECK_VERSION}" >> params.txt 
+    echo -e "Haplogrep\t\${HAPLOGREP_VERSION}" >> params.txt 
 
     #TODO: split fwd and reverse? https://bioinformatics.stackexchange.com/questions/8649/how-can-i-calculate-coverage-at-single-bases-using-a-bam-file
+
+    # Extract the value of Contig and store it in a variable
+    contig=`awk '\$2 == "Contig" {print \$3; exit}' "${statistics}"`
+
     echo -e "Contig\tPosition\tCoverage" > coverage.tsv
-    samtools depth -a  ${sample_bam_file} >> coverage.tsv
+    samtools index ${sample_bam_file}
+    samtools depth -a  ${sample_bam_file} -r \$contig >> coverage.tsv
 
     Rscript -e "require('rmarkdown'); render('${report}',
     params = list(

reports/report.Rmd

@@ -4,7 +4,8 @@ output:
   flexdashboard::flex_dashboard:
     orientation: rows
     navbar:
-      - { title: "About", href: "https://mitoverse.i-med.ac.at/#!pages/contact", align: right }
+      - { title: "MultiQC", target: "_blank", href: "multiqc/index.html" }
+      - { title: "About",  target: "_blank", href: "https://mitoverse.i-med.ac.at/#!pages/contact", align: right }
 params:
   haplogroups: ../tests/data/report/haplogroups.txt
   haplocheck: ../tests/data/report/haplocheck.txt

reports/sample.Rmd

@@ -191,6 +191,7 @@ variants %>%
   mutate(
     Variant_Label = link_to_variant(Pos, Ref, Variant)
   ) %>% 
+  arrange(Pos, Ref, Variant) %>%
   select("Variant_Label", "VariantLevel", "Type_Label") %>%
   datatable(
     colnames=c("Variant", "Level", ""),
@@ -206,3 +207,18 @@ variants %>%
     class = 'cell-border stripe'
   )
 ```
+
+
+### Paramteres and Software Version
+
+```{r}
+pipeline_params %>%
+  kable()
+```
+
+
+---
+
+<small>
+This report has been created with **[mtDNA-Server 2](https://mitoverse.i-med.ac.at)**, a nextflow pipeline developed by [Sebastian Schönherr](mailto:[email protected]), [Hansi Weissensteiner](mailto:[email protected]) and [Lukas Forer](mailto:[email protected]), Institute of Genetic Epidemiology, Medical University of Innsbruck.
+</small>

tests/mitocalling.nf.test.snap

@@ -3,29 +3,90 @@
         "content": [
             "variants.annotated.txt:md5,52dc3737a73bb80cf3a1c8946990c3e4"
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
         "timestamp": "2024-03-02T13:11:34.901277407"
     },
+    "Runs with 6 samples provided as testdata with mutect2": {
+        "content": [
+            "variants.annotated.txt:md5,d5bcadb427d40ffc53a118bcd9bc5aae",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 28,
+                "tasksSucceeded": 28
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T14:11:30.627373"
+    },
     "Runs with single BAM file and mutserve": {
         "content": [
             "variants.annotated.txt:md5,ee00b39fc49e1f34e6affab00368181f"
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
         "timestamp": "2024-03-02T13:09:45.954385792"
     },
     "Runs with BAM file including different header contigs": {
         "content": [
             "variants.annotated.txt:md5,a5345c7718757ded27246ae342b5f25b"
         ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
         "timestamp": "2024-03-02T13:10:28.843431233"
     },
     "Runs with two files and one goes through QC": {
         "content": [
             "variants.annotated.txt:md5,ef402762b03356a208583e434d96dfa3",
             {
                 "tasksFailed": 0,
-                "tasksCount": 10,
-                "tasksSucceeded": 10
+                "tasksCount": 12,
+                "tasksSucceeded": 12
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T14:02:05.743122"
+    },
+    "Runs with 6 samples provided as testdata with fusion": {
+        "content": [
+            "variants.annotated.txt:md5,5043504edb7e0bf5492fafb63e64daa6",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 40,
+                "tasksSucceeded": 40
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T14:15:40.016064"
+    },
+    "Runs with 6 samples provided as testdata with mutserve": {
+        "content": [
+            "variants.annotated.txt:md5,d383a9cb2a1f46c96770390c61002bfc",
+            {
+                "tasksFailed": 0,
+                "tasksCount": 30,
+                "tasksSucceeded": 30
             }
         ],
-        "timestamp": "2024-03-02T13:12:29.64633988"
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.04.3"
+        },
+        "timestamp": "2024-03-02T14:08:07.908258"
     }
 }