Merge pull request #155 from supernifty/coverage-thresholds

add customisable QC thresholds
MelbourneGenomics · Jul 26, 2016 · 2a0a29b · 2a0a29b
2 parents ea0edb3 + d59408b
commit 2a0a29b
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diff --git a/pipeline/config.groovy.template b/pipeline/config.groovy.template
@@ -268,3 +268,14 @@ TRIO_REFINEMENT_SUPPORTING="$REFBASE/1000G_phase3_v4_20130502.sites.hg19.vcf.gz"
 // generate a filtered bam file. options are exons, design, or skip
 FILTERED_ON_EXONS="skip"
 
+////////////////////////////////////////////
+// qc options
+////////////////////////////////////////////
+// what depth is required to contribute to satisfactory coverage
+QC_THRESHOLD=20
+// what percentage of QC_THRESHOLD must be achieved across the gene to get a good rating
+QC_GOOD=95
+// what percentage of QC_THRESHOLD must be achieved across the gene to get a pass rating
+QC_PASS=80
+// what percentage of QC_THRESHOLD must be achieved across the gene to get a fail rating
+QC_FAIL=0
diff --git a/pipeline/pipeline_stage_reports.groovy b/pipeline/pipeline_stage_reports.groovy
@@ -185,7 +185,7 @@ summary_report = {
     produce("${run_id}_${sample}.summary.htm", "${run_id}_${sample}.summary.md", "${run_id}_${sample}.summary.karyotype.tsv") {
         from("$input_exome_file", "$input_ontarget_file", "$input_fragments_file") {
             exec """
-                python $SCRIPTS/qc_report.py --report_cov $input_coverage_file --exome_cov $input_exome_file --ontarget $input_ontarget_file ${inputs.metrics.withFlag("--metrics")} --study $sample --meta $sample_metadata_file --threshold 20 --classes GOOD:95:GREEN,PASS:80:ORANGE,FAIL:0:RED --gc $target_gene_file --gene_cov qc/exon_coverage_stats.txt --write_karyotype $output.tsv --fragments $input_fragments_file --padding $INTERVAL_PADDING_CALL,$INTERVAL_PADDING_INDEL,$INTERVAL_PADDING_SNV > $output.md
+                python $SCRIPTS/qc_report.py --report_cov $input_coverage_file --exome_cov $input_exome_file --ontarget $input_ontarget_file ${inputs.metrics.withFlag("--metrics")} --study $sample --meta $sample_metadata_file --threshold $QC_THRESHOLD --classes GOOD:$QC_GOOD:GREEN,PASS:$QC_PASS:ORANGE,FAIL:$QC_FAIL:RED --gc $target_gene_file --gene_cov qc/exon_coverage_stats.txt --write_karyotype $output.tsv --fragments $input_fragments_file --padding $INTERVAL_PADDING_CALL,$INTERVAL_PADDING_INDEL,$INTERVAL_PADDING_SNV > $output.md
 
                 python $SCRIPTS/markdown2.py --extras tables < $output.md | python $SCRIPTS/prettify_markdown.py > $output.htm
             """