{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk-protected/pulls/comments/63733732","id":63733732,"diff_hunk":"@@ -0,0 +1,304 @@\n+#\n+# Workflow a single pair of case-control samples.\n+#\n+# Notes:\n+#\n+# - file names will use the entity ID specified, but inside the file, the bam SM tag will typically be used.\n+#\n+# - THIS SCRIPT SHOULD BE CONSIDERED OF \"BETA\" QUALITY\n+#\n+# - For jni_lib values, see README.  For example, Ubuntu: /usr/lib/jni\n+#\n+###########\n+\n+workflow case_gatk_acnv_workflow {\n+    String wf_entity_id_tumor\n+    String wf_entity_id_normal\n+    File target_bed\n+    File ref_fasta\n+    File ref_fasta_dict\n+    File ref_fasta_fai\n+    File common_snp_list\n+    File tumor_bam\n+    File tumor_bam_idx\n+    File normal_bam\n+    File normal_bam_idx\n+    File jar_file\n+    File PoN\n+    String is_disable_reference_validation\n+    File jni_lib    \n+\n+  call PadTargets {\n+    input:\n+        target_bed=target_bed,\n+        jar_file=jar_file,\n+        mem=1\n+  }\n+\n+  call CalculateTargetCoverage as TumorCalculateTargetCoverage {\n+    input:\n+        entity_id=wf_entity_id_tumor,\n+        padded_target_bed=PadTargets.padded_target_bed,\n+        input_bam=tumor_bam,\n+        ref_fasta=ref_fasta,\n+        ref_fasta_fai=ref_fasta_fai,\n+        ref_fasta_dict=ref_fasta_dict,\n+        jar_file=jar_file,\n+        disable_reference_validation=is_disable_reference_validation,\n+        mem=2\n+\n+  }\n+\n+  call NormalizeSomaticReadCounts as TumorNormalizeSomaticReadCounts {\n+    input:\n+        entity_id=wf_entity_id_tumor,\n+        coverage_file=TumorCalculateTargetCoverage.gatk_cnv_coverage_file,\n+        padded_target_bed=PadTargets.padded_target_bed,\n+        pon=PoN,\n+        jar_file=jar_file,\n+        mem=2,\n+\tjni_lib=jni_lib\n+  }\n+\n+  call PerformSegmentation as TumorPerformSeg{\n+    input:\n+        entity_id=wf_entity_id_tumor,\n+        jar_file=jar_file,\n+        tn_file=TumorNormalizeSomaticReadCounts.tn_file,\n+        mem=2\n+  }\n+\n+  call Caller as TumorCaller {\n+    input:\n+        entity_id=wf_entity_id_tumor,\n+        jar_file=jar_file,\n+        tn_file=TumorNormalizeSomaticReadCounts.tn_file,\n+        seg_file=TumorPerformSeg.seg_file,\n+        mem=2\n+  }\n+\n+  call CalculateTargetCoverage as NormalCalculateTargetCoverage {\n+    input:\n+        entity_id=wf_entity_id_normal,\n+        padded_target_bed=PadTargets.padded_target_bed,\n+        input_bam=tumor_bam,\n+        ref_fasta=ref_fasta,\n+        ref_fasta_fai=ref_fasta_fai,\n+        ref_fasta_dict=ref_fasta_dict,\n+        jar_file=jar_file,\n+        disable_reference_validation=is_disable_reference_validation,\n+        mem=2\n+\n+  }\n+\n+  call NormalizeSomaticReadCounts as NormalNormalizeSomaticReadCounts {\n+    input:\n+        entity_id=wf_entity_id_normal,\n+        coverage_file=NormalCalculateTargetCoverage.gatk_cnv_coverage_file,\n+        padded_target_bed=PadTargets.padded_target_bed,\n+        pon=PoN,\n+        jar_file=jar_file,\n+        mem=2,\n+\tjni_lib=jni_lib\n+  }\n+\n+  call PerformSegmentation as NormalPerformSeg {\n+    input:\n+        entity_id=wf_entity_id_normal,\n+        jar_file=jar_file,\n+        tn_file=NormalNormalizeSomaticReadCounts.tn_file,\n+        mem=2\n+  }\n+\n+  call Caller as NormalCaller {\n+    input:\n+        entity_id=wf_entity_id_normal,\n+        jar_file=jar_file,\n+        tn_file=NormalNormalizeSomaticReadCounts.tn_file,\n+        seg_file=NormalPerformSeg.seg_file,\n+        mem=2\n+  }\n+\n+  call HetPulldown {\n+    input:\n+        entity_id_tumor=wf_entity_id_tumor,\n+        entity_id_normal=wf_entity_id_normal,\n+        jar_file=jar_file,\n+        mem = 4,\n+        ref_fasta=ref_fasta,\n+        ref_fasta_fai=ref_fasta_fai,\n+        ref_fasta_dict=ref_fasta_dict,\n+        tumor_bam=tumor_bam,\n+        tumor_bam_idx=tumor_bam_idx,\n+        normal_bam=normal_bam,\n+        normal_bam_idx=normal_bam_idx,\n+        common_snp_list=common_snp_list\n+  }\n+\n+  call AllelicCNV {\n+    input:\n+        entity_id=wf_entity_id_tumor,\n+        jar_file=jar_file,\n+        mem=4,\n+        tumor_hets=HetPulldown.tumor_hets,\n+        called_file=TumorCaller.called_file,\n+        tn_file=TumorNormalizeSomaticReadCounts.tn_file\n+  }\n+}\n+\n+# Pad the target file.  This was found to help sensitivity and specificity.  This step should only be altered\n+#  by advanced users.  Note that by changing this, you need to have a PoN that also reflects the change.\n+task PadTargets {\n+    File target_bed\n+    Int pd = 250\n+    Int mem\n+    File jar_file\n+    command {\n+        java -Xmx${mem}g -jar ${jar_file} PadTargets  --targets ${target_bed} --output targets.padded.bed --padding ${pd}  --help false --version false --verbosity INFO --QUIET false\n+    }\n+    output {\n+        File padded_target_bed = \"targets.padded.bed\"\n+    }\n+    #runtime {\n+    #    docker: \"gatk-protected/a1\"\n+    #}\n+}\n+\n+# Calculate the target coverage\n+task CalculateTargetCoverage {\n+    String entity_id\n+    File padded_target_bed\n+    String transform = \"PCOV\"\n+    String grouping = \"SAMPLE\"\n+    Boolean keepduplicatereads = true\n+    Boolean disable_all_read_filters = false\n+    File input_bam\n+    File ref_fasta\n+    File ref_fasta_fai\n+    File ref_fasta_dict\n+    Int mem\n+    File jar_file\n+    String disable_reference_validation\n+\n+    command {\n+        java -Xmx${mem}g -jar ${jar_file} CalculateTargetCoverage --output ${entity_id}.coverage.tsv --groupBy ${grouping} --transform ${transform} --targets ${padded_target_bed} --targetInformationColumns FULL --keepduplicatereads ${keepduplicatereads} --input ${input_bam} --reference ${ref_fasta}  --disable_all_read_filters ${disable_all_read_filters} --interval_set_rule UNION --interval_padding 0 --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation ${disable_reference_validation} --createOutputBamIndex true --help false --version false --verbosity INFO --QUIET false\n+    }\n+    output {\n+        File gatk_cnv_coverage_file = \"${entity_id}.coverage.tsv\"\n+    }\n+\n+    #runtime {\n+    #    docker: \"gatk-protected/a1\"\n+    #}\n+}\n+\n+task NormalizeSomaticReadCounts {\n+    String entity_id\n+    File coverage_file\n+    File padded_target_bed\n+    File pon\n+    Int mem\n+    File jar_file\n+    File jni_lib\n+    command {\n+        java -Xmx${mem}g -Djava.library.path=${jni_lib} -jar ${jar_file} NormalizeSomaticReadCounts  --input ${coverage_file} \\\n+        --targets ${padded_target_bed} --panelOfNormals ${pon} --factorNormalizedOutput ${entity_id}.fnt.tsv --tangentNormalized ${entity_id}.tn.tsv \\\n+        --betaHatsOutput ${entity_id}.betaHats.tsv --preTangentNormalized  ${entity_id}.preTN.tsv  --help false --version false --verbosity INFO --QUIET false\n+    }\n+\n+    output {\n+        File tn_file = \"${entity_id}.tn.tsv\"\n+        File pre_tn_file = \"${entity_id}.preTN.tsv\"\n+        File betahats_file = \"${entity_id}.betaHats.tsv\"\n+    }\n+    #runtime {\n+    #    docker: \"gatk-protected/a1\"\n+    #}\n+}\n+\n+task PerformSegmentation {\n+    Int mem\n+    String entity_id\n+    File jar_file\n+    File tn_file\n+\n+    command {\n+        java -Xmx${mem}g -jar ${jar_file} PerformSegmentation  --targets ${tn_file} \\\n+        --output ${entity_id}.seg --log2Input true  --alpha 0.01 --nperm 10000 --pmethod HYBRID --minWidth 2 --kmax 25 \\\n+        --nmin 200 --eta 0.05 --trim 0.025 --undoSplits NONE --undoPrune 0.05 --undoSD 3 --help false --version false \\\n+        --verbosity INFO --QUIET false\n+    }\n+\n+    output {\n+        File seg_file = \"${entity_id}.seg\"\n+    }\n+}\n+\n+task Caller {\n+    Int mem\n+    String entity_id\n+    File jar_file\n+    File tn_file\n+    File seg_file\n+\n+    command {\n+        java -Xmx${mem}g -jar ${jar_file} CallSegments  --targets ${tn_file} \\\n+         --segments ${seg_file} --output ${entity_id}.called --threshold 2.0  --legacy false --experimental false \\\n+          --help false --version false --verbosity INFO --QUIET false\n+    }\n+\n+    output {\n+        File called_file=\"${entity_id}.called\"\n+    }\n+}\n+\n+# entity IDs can be the same value\n+task HetPulldown {\n+    String entity_id_tumor\n+    String entity_id_normal\n+    File jar_file\n+    Int mem\n+    File ref_fasta\n+    File ref_fasta_fai\n+    File ref_fasta_dict\n+    File tumor_bam\n+    File tumor_bam_idx\n+    File normal_bam\n+    File normal_bam_idx\n+    File common_snp_list\n+\n+    command {\n+        java -Xmx${mem}g -jar ${jar_file} GetHetCoverage  --reference ${ref_fasta} \\\n+        --normal ${normal_bam} --tumor ${tumor_bam} --snpIntervals ${common_snp_list}  \\\n+        --normalHets ${entity_id_normal}.normal.hets.tsv --tumorHets ${entity_id_tumor}.tumor.hets.tsv --pvalueThreshold 0.05 \\\n+        --help false --version false --verbosity INFO --QUIET false --VALIDATION_STRINGENCY LENIENT\n+    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