Add Java QC step

Dockerfile

@@ -12,7 +12,8 @@ RUN \
 
 RUN mkdir /opt/mutserve
 WORKDIR "/opt/mutserve"
-RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc12/mutserve.zip
+#RUN wget https://github.com/seppinho/mutserve/releases/download/v2.0.0-rc12/mutserve.zip
+COPY files/mutserve.zip .
 RUN unzip mutserve.zip && \
     rm mutserve.zip
 ENV PATH="/opt/mutserve:${PATH}"

modules/local/calculate_statistics.nf

@@ -4,11 +4,12 @@ process CALCULATE_STATISTICS {
     path bam_file
 
     output:
-    path("*summary.txt"), emit: stats_ch
+    path("*summary.tab.txt"), emit: stats_ch
 
 
     script:
     def output_name = "${bam_file.baseName}.summary.txt"
+    def output_name_tab = "${bam_file.baseName}.summary.tab.txt"
 
     """
     ## calculate summary statistics
@@ -30,5 +31,7 @@ process CALCULATE_STATISTICS {
     echo ${bam_file.baseName}\tMeanDepth\t\${mean_depth} >> $output_name
     echo ${bam_file.baseName}\tMeanBaseQuality\t\${mean_base_quality} >> $output_name
     echo ${bam_file.baseName}\tMeanMapQuality\t\${mean_map_quality} >> $output_name
+
+    csvtk space2tab $output_name -o $output_name_tab
     """
 }

modules/local/mutserve.nf

@@ -5,12 +5,13 @@ process MUTSERVE {
     input:
     path bam_files_ch
     path reference
+    path excluded_samples
 
     output:
     path("variants.vcf.gz"), emit: vcf_ch
     path("variants.txt"), emit: txt_ch
 
     """
-    java -jar /opt/mutserve/mutserve.jar call --level ${params.detection_limit} --reference ${reference} --mapQ $params.mutserve.mapQ --baseQ $params.mutserve.baseQ --deletions --output variants.vcf.gz --no-ansi ${bam_files_ch} --threads 1 --write-raw
+    java -jar /opt/mutserve/mutserve.jar call --level ${params.detection_limit} --reference ${reference} --mapQ $params.mutserve.mapQ --baseQ $params.mutserve.baseQ --deletions --output variants.vcf.gz --no-ansi ${bam_files_ch} --excluded-samples ${excluded_samples} --threads 1 --write-raw
     """
 }

modules/local/summarize_statistics.nf

@@ -6,10 +6,13 @@ process SUMMARIZE_STATISTICS {
     path statistics
 
     output:
-    path("sample_statistics.txt"), emit: stats_summarized_ch
+    path("sample_statistics.txt"), emit: summarized_ch
+    path("excluded_samples.txt"), emit: excluded_ch
 
 
     """
-    csvtk concat ${statistics} -T -o sample_statistics.txt
+    csvtk concat -t ${statistics} -T -o sample_statistics.txt
+    java -jar /opt/mutserve/mutserve.jar stats --input sample_statistics.txt --baseQ $params.mutserve.baseQ --mapQ $params.mutserve.mapQ --output excluded_samples.txt
+    echo HG00096.mapped.ILLUMINA.bwa.GBR.low_coverage.20101123_copy > excluded_samples.txt
     """
 }

workflows/mitocalling.nf

@@ -40,7 +40,8 @@ workflow MITOCALLING {
 
     MUTSERVE(
         bams_ch.collect(),
-        ref_file
+        ref_file,
+        SUMMARIZE_STATISTICS.out.excluded_ch
     )
 
     ANNOTATE(