From 5e520314dd766b4d8aad35fa4906affd006e16d3 Mon Sep 17 00:00:00 2001
From: Sebastian Schoenherr <sebastian.schoenherr@i-med.ac.at>
Date: Mon, 4 Mar 2024 14:21:42 +0100
Subject: [PATCH] Set name to coverage estimation

---
 Dockerfile                                                | 4 ++--
 bin/{CoverageCorrection.java => CoverageEstimation.java}  | 4 ++--
 cloudgene.yaml                                            | 7 +++++--
 .../{coverage_correction.nf => coverage_estimation.nf}    | 4 ++--
 nextflow.config                                           | 3 +--
 workflows/mtdna_server_2.nf                               | 8 ++++----
 6 files changed, 16 insertions(+), 14 deletions(-)
 rename bin/{CoverageCorrection.java => CoverageEstimation.java} (95%)
 rename modules/local/{coverage_correction.nf => coverage_estimation.nf} (76%)

diff --git a/Dockerfile b/Dockerfile
index 248c2f0..b0d60d9 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -63,7 +63,7 @@ WORKDIR "/opt"
 COPY ./bin/VariantMerger.java ./
 RUN jbang export portable -O=VariantMerger.jar VariantMerger.java
 
-COPY ./bin/CoverageCorrection.java ./
-RUN jbang export portable -O=CoverageCorrection.jar CoverageCorrection.java
+COPY ./bin/CoverageEstimation.java ./
+RUN jbang export portable -O=CoverageEstimation.jar CoverageEstimation.java
 
 
diff --git a/bin/CoverageCorrection.java b/bin/CoverageEstimation.java
similarity index 95%
rename from bin/CoverageCorrection.java
rename to bin/CoverageEstimation.java
index f4f52a6..75184ba 100644
--- a/bin/CoverageCorrection.java
+++ b/bin/CoverageEstimation.java
@@ -13,7 +13,7 @@
 import picocli.CommandLine;
 import picocli.CommandLine.Option;
 
-public class CoverageCorrection implements Callable<Integer> {
+public class CoverageEstimation implements Callable<Integer> {
 
 	@Option(names = "--input", description = "Input Variants File", required = true)
 	private String input;
@@ -68,7 +68,7 @@ public Integer call() throws Exception {
 	}
 
 	public static void main(String... args) {
-		int exitCode = new CommandLine(new CoverageCorrection()).execute(args);
+		int exitCode = new CommandLine(new CoverageEstimation()).execute(args);
 		System.exit(exitCode);
 	}
 
diff --git a/cloudgene.yaml b/cloudgene.yaml
index 4f65112..0abd942 100644
--- a/cloudgene.yaml
+++ b/cloudgene.yaml
@@ -49,6 +49,9 @@ workflow:
         - process: "MTDNA_SERVER_2:ANNOTATE"
           label: "Annotation"
           view: progressbar
+        - process: "MTDNA_SERVER_2:COVERAGE_ESTIMATION"
+          label: "Calculating VAF Coverage"
+          view: progressbar          
         - process: "MTDNA_SERVER_2:HAPLOGROUPS_CONTAMINATION"
           label: "Haplogroup % Contamination Detection"
           view: progressbar
@@ -82,8 +85,8 @@ workflow:
         0.05: 0.05
         0.1: 0.1      
 
-    - id: coverage_correction
-      description: Coverage Correction for Diagnostic NGS
+    - id: coverage_estimation
+      description: Coverage Estimation for Diagnostic NGS
       type: list
       value: off
       values:
diff --git a/modules/local/coverage_correction.nf b/modules/local/coverage_estimation.nf
similarity index 76%
rename from modules/local/coverage_correction.nf
rename to modules/local/coverage_estimation.nf
index c1ca15f..0ff5fcf 100644
--- a/modules/local/coverage_correction.nf
+++ b/modules/local/coverage_estimation.nf
@@ -1,4 +1,4 @@
-process COVERAGE_CORRECTION {
+process COVERAGE_ESTIMATION {
 
     input:
     path variants_txt
@@ -7,7 +7,7 @@ process COVERAGE_CORRECTION {
     path("variants.txt"), emit: variants_verified_ch
 
     """
-    java -jar /opt/CoverageCorrection.jar \
+    java -jar /opt/CoverageEstimation.jar \
         --input ${variants_txt} \
         --output variants.verified.txt
     mv variants.verified.txt variants.txt     
diff --git a/nextflow.config b/nextflow.config
index e638843..bdc8866 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -21,8 +21,7 @@ params {
     mapQ                   = 20
     baseQ                  = 20
     alignQ                 = 30
-    high_accuracy          = true
-    coverage_correction    = "on"
+    coverage_estimation    = "on"
     max_samples            = 0
 
 
diff --git a/workflows/mtdna_server_2.nf b/workflows/mtdna_server_2.nf
index 1103693..b66862d 100644
--- a/workflows/mtdna_server_2.nf
+++ b/workflows/mtdna_server_2.nf
@@ -26,7 +26,7 @@ include { MERGING_VARIANTS } from '../modules/local/merging_variants'
 include { VCF_MERGE } from '../modules/local/vcf_merge'
 include { ANNOTATE } from '../modules/local/annotate'
 include { HAPLOGROUPS_CONTAMINATION } from '../modules/local/haplogroups_contamination'
-include { COVERAGE_CORRECTION } from '../modules/local/coverage_correction'
+include { COVERAGE_ESTIMATION } from '../modules/local/coverage_estimation'
 include { REPORT } from '../modules/local/report'
 include { SAMPLE_REPORT } from '../modules/local/sample_report'
 
@@ -164,11 +164,11 @@ workflow MTDNA_SERVER_2 {
         contamination_ch =  HAPLOGROUPS_CONTAMINATION.out.contamination_txt_ch
     }
 
-    if (params.coverage_correction.equals("on") && params.mode != 'mutect2') {
-        COVERAGE_CORRECTION(
+    if (params.coverage_estimation.equals("on") && params.mode != 'mutect2') {
+        COVERAGE_ESTIMATION(
             variants_txt_ch
         )
-        variants_txt_ch = COVERAGE_CORRECTION.out.variants_verified_ch
+        variants_txt_ch = COVERAGE_ESTIMATION.out.variants_verified_ch
     }    
     
     ANNOTATE(