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workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"job_uuid\" [fillcolor=\"#94DDF4\",label=\"job_uuid\"];\n    \"input_bam\" [fillcolor=\"#94DDF4\",label=\"input_bam\"];\n    \"thread_count\" [fillcolor=\"#94DDF4\",label=\"thread_count\"];\n    \"reference_sequence\" [fillcolor=\"#94DDF4\",label=\"reference_sequence\"];\n    \"known_snp\" [fillcolor=\"#94DDF4\",label=\"known_snp\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"sqlite\" [fillcolor=\"#94DDF4\",label=\"sqlite\"];\n    \"bam\" [fillcolor=\"#94DDF4\",label=\"bam\"];\n  }\n  \"fastqc_db_o1\" [label=\"fastqc_db_o1\"];\n  \"bwa_o1\" [label=\"bwa_o1\"];\n  \"picard_sortsam_o1\" [label=\"picard_sortsam_o1\"];\n  \"fastqc_o1\" [label=\"fastqc_o1\"];\n  \"metrics_bqsr\" [label=\"metrics_bqsr\", fillcolor=\"#F3CEA1\"];\n  \"bam_reheader\" [label=\"bam_reheader\"];\n  \"sort_scattered_fastq_o1\" [label=\"sort_scattered_fastq_o1\"];\n  \"readgroup_json_db\" [label=\"readgroup_json_db\"];\n  \"fastqc_db_s\" [label=\"fastqc_db_s\"];\n  \"bam_readgroup_to_json\" [label=\"bam_readgroup_to_json\"];\n  \"fastqc_o1_basicstats_json\" [label=\"fastqc_o1_basicstats_json\"];\n  \"picard_markduplicates_to_sqlite\" [label=\"picard_markduplicates_to_sqlite\"];\n  \"sort_scattered_fastq_s\" [label=\"sort_scattered_fastq_s\"];\n  \"merge_all_sqlite\" [label=\"merge_all_sqlite\"];\n  \"picard_validatesamfile_original\" [label=\"picard_validatesamfile_original\"];\n  \"fastqc2\" [label=\"fastqc2\"];\n  \"sort_scattered_fastq2\" [label=\"sort_scattered_fastq2\"];\n  \"merge_fastqc_db_o2_sqlite\" [label=\"merge_fastqc_db_o2_sqlite\"];\n  \"remove_duplicate_fastq2\" [label=\"remove_duplicate_fastq2\"];\n  \"picard_validatesamfile_original_to_sqlite\" [label=\"picard_validatesamfile_original_to_sqlite\"];\n  \"integrity\" [label=\"integrity\", fillcolor=\"#F3CEA1\"];\n  \"gatk_applybqsr\" [label=\"gatk_applybqsr\"];\n  \"picard_validatesamfile_bqsr\" [label=\"picard_validatesamfile_bqsr\"];\n  \"biobambam_bamtofastq\" [label=\"biobambam_bamtofastq\"];\n  \"fastqc1\" [label=\"fastqc1\"];\n  \"sort_scattered_fastq1\" [label=\"sort_scattered_fastq1\"];\n  \"merge_fastqc_db2_sqlite\" [label=\"merge_fastqc_db2_sqlite\"];\n  \"picard_mergesamfiles_se\" [label=\"picard_mergesamfiles_se\"];\n  \"picard_mergesamfiles_o2\" [label=\"picard_mergesamfiles_o2\"];\n  \"decider_bwa_se\" [label=\"decider_bwa_se\"];\n  \"decider_bwa_o2\" [label=\"decider_bwa_o2\"];\n  \"remove_duplicate_fastq1\" [label=\"remove_duplicate_fastq1\"];\n  \"merge_fastqc_db_o1_sqlite\" [label=\"merge_fastqc_db_o1_sqlite\"];\n  \"fastqc_db2\" [label=\"fastqc_db2\"];\n  \"merge_readgroup_json_db\" [label=\"merge_readgroup_json_db\"];\n  \"remove_duplicate_fastq_s\" [label=\"remove_duplicate_fastq_s\"];\n  \"remove_duplicate_fastq_o2\" [label=\"remove_duplicate_fastq_o2\"];\n  \"fastqc_o2_basicstats_json\" [label=\"fastqc_o2_basicstats_json\"];\n  \"fastqc_db_o2\" [label=\"fastqc_db_o2\"];\n  \"picard_mergesamfiles_pe\" [label=\"picard_mergesamfiles_pe\"];\n  \"fastqc_s\" [label=\"fastqc_s\"];\n  \"gatk_baserecalibrator\" [label=\"gatk_baserecalibrator\"];\n  \"bwa_se\" [label=\"bwa_se\"];\n  \"picard_sortsam_se\" [label=\"picard_sortsam_se\"];\n  \"bwa_o2\" [label=\"bwa_o2\"];\n  \"picard_sortsam_o2\" [label=\"picard_sortsam_o2\"];\n  \"decider_bwa_pe\" [label=\"decider_bwa_pe\"];\n  \"picard_markduplicates\" [label=\"picard_markduplicates\"];\n  \"fastqc_o2\" [label=\"fastqc_o2\"];\n  \"samtools_bamtobam\" [label=\"samtools_bamtobam\"];\n  \"picard_validatesamfile_bqsr_to_sqlite\" [label=\"picard_validatesamfile_bqsr_to_sqlite\"];\n  \"picard_mergesamfiles_o1\" [label=\"picard_mergesamfiles_o1\"];\n  \"picard_sortsam_pe\" [label=\"picard_sortsam_pe\"];\n  \"bwa_pe\" [label=\"bwa_pe\"];\n  \"fastqc_pe_basicstats_json\" [label=\"fastqc_pe_basicstats_json\"];\n  \"sort_scattered_fastq_o2\" [label=\"sort_scattered_fastq_o2\"];\n  \"merge_fastqc_db1_sqlite\" [label=\"merge_fastqc_db1_sqlite\"];\n  \"decider_bwa_o1\" [label=\"decider_bwa_o1\"];\n  \"picard_mergesamfiles\" [label=\"picard_mergesamfiles\"];\n  \"fastqc_db1\" [label=\"fastqc_db1\"];\n  \"remove_duplicate_fastq_o1\" [label=\"remove_duplicate_fastq_o1\"];\n  \"merge_fastqc_db_s_sqlite\" [label=\"merge_fastqc_db_s_sqlite\"];\n  \"fastqc_se_basicstats_json\" [label=\"fastqc_se_basicstats_json\"];\n  \"job_uuid\" -> \"fastqc_db_o1\" [label=\"job_uuid\"];\n  \"fastqc_o1\" -> \"fastqc_db_o1\" [label=\"INPUT\"];\n  \"thread_count\" -> \"bwa_o1\" [label=\"thread_count\"];\n  \"decider_bwa_o1\" -> \"bwa_o1\" [label=\"readgroup_json_path\"];\n  \"fastqc_o1_basicstats_json\" -> \"bwa_o1\" [label=\"fastqc_json_path\"];\n  \"sort_scattered_fastq_o1\" -> \"bwa_o1\" [label=\"fastq\"];\n  \"reference_sequence\" -> \"bwa_o1\" [label=\"fasta\"];\n  \"bwa_o1\" -> \"picard_sortsam_o1\" [label=\"INPUT\"];\n  \"sort_scattered_fastq_o1\" -> \"fastqc_o1\" [label=\"INPUT\"];\n  \"thread_count\" -> \"fastqc_o1\" [label=\"threads\"];\n  \"thread_count\" -> \"metrics_bqsr\" [label=\"thread_count\"];\n  \"known_snp\" -> \"metrics_bqsr\" [label=\"known_snp\"];\n  \"job_uuid\" -> \"metrics_bqsr\" [label=\"job_uuid\"];\n  \"reference_sequence\" -> \"metrics_bqsr\" [label=\"fasta\"];\n  \"gatk_applybqsr\" -> \"metrics_bqsr\" [label=\"bam\"];\n  \"picard_mergesamfiles\" -> \"bam_reheader\" [label=\"input\"];\n  \"remove_duplicate_fastq_o1\" -> \"sort_scattered_fastq_o1\" [label=\"INPUT\"];\n  \"bam_readgroup_to_json\" -> \"readgroup_json_db\" [label=\"json_path\"];\n  \"job_uuid\" -> \"readgroup_json_db\" [label=\"job_uuid\"];\n  \"job_uuid\" -> \"fastqc_db_s\" [label=\"job_uuid\"];\n  \"fastqc_s\" -> \"fastqc_db_s\" [label=\"INPUT\"];\n  \"samtools_bamtobam\" -> \"bam_readgroup_to_json\" [label=\"INPUT\"];\n  \"merge_fastqc_db_o1_sqlite\" -> \"fastqc_o1_basicstats_json\" [label=\"sqlite_path\"];\n  \"picard_markduplicates\" -> \"picard_markduplicates_to_sqlite\" [label=\"metric_path\"];\n  \"job_uuid\" -> \"picard_markduplicates_to_sqlite\" [label=\"job_uuid\"];\n  \"picard_markduplicates\" -> \"picard_markduplicates_to_sqlite\" [label=\"bam\"];\n  \"remove_duplicate_fastq_s\" -> \"sort_scattered_fastq_s\" [label=\"INPUT\"];\n  \"merge_fastqc_db1_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"metrics_bqsr\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"picard_markduplicates_to_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"merge_fastqc_db_o2_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"merge_fastqc_db_o1_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"picard_validatesamfile_original_to_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"integrity\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"merge_fastqc_db2_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"merge_fastqc_db_s_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"merge_readgroup_json_db\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"picard_validatesamfile_bqsr_to_sqlite\" -> \"merge_all_sqlite\" [label=\"source_sqlite\"];\n  \"job_uuid\" -> \"merge_all_sqlite\" [label=\"job_uuid\"];\n  \"samtools_bamtobam\" -> \"picard_validatesamfile_original\" [label=\"INPUT\"];\n  \"thread_count\" -> \"fastqc2\" [label=\"threads\"];\n  \"sort_scattered_fastq2\" -> \"fastqc2\" [label=\"INPUT\"];\n  \"remove_duplicate_fastq2\" -> \"sort_scattered_fastq2\" [label=\"INPUT\"];\n  \"fastqc_db_o2\" -> \"merge_fastqc_db_o2_sqlite\" [label=\"source_sqlite\"];\n  \"job_uuid\" -> \"merge_fastqc_db_o2_sqlite\" [label=\"job_uuid\"];\n  \"biobambam_bamtofastq\" -> \"remove_duplicate_fastq2\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"picard_validatesamfile_original_to_sqlite\" [label=\"job_uuid\"];\n  \"input_bam\" -> \"picard_validatesamfile_original_to_sqlite\" [label=\"bam\"];\n  \"picard_validatesamfile_original\" -> \"picard_validatesamfile_original_to_sqlite\" [label=\"metric_path\"];\n  \"job_uuid\" -> \"integrity\" [label=\"job_uuid\"];\n  \"gatk_applybqsr\" -> \"integrity\" [label=\"bam\"];\n  \"gatk_applybqsr\" -> \"integrity\" [label=\"bai\"];\n  \"picard_markduplicates\" -> \"gatk_applybqsr\" [label=\"input\"];\n  \"gatk_baserecalibrator\" -> \"gatk_applybqsr\" [label=\"bqsr-recal-file\"];\n  \"gatk_applybqsr\" -> \"picard_validatesamfile_bqsr\" [label=\"INPUT\"];\n  \"samtools_bamtobam\" -> \"biobambam_bamtofastq\" [label=\"filename\"];\n  \"sort_scattered_fastq1\" -> \"fastqc1\" [label=\"INPUT\"];\n  \"thread_count\" -> \"fastqc1\" [label=\"threads\"];\n  \"remove_duplicate_fastq1\" -> \"sort_scattered_fastq1\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"merge_fastqc_db2_sqlite\" [label=\"job_uuid\"];\n  \"fastqc_db2\" -> \"merge_fastqc_db2_sqlite\" [label=\"source_sqlite\"];\n  \"input_bam\" -> \"picard_mergesamfiles_se\" [label=\"OUTPUT\"];\n  \"picard_sortsam_se\" -> \"picard_mergesamfiles_se\" [label=\"INPUT\"];\n  \"picard_sortsam_o2\" -> \"picard_mergesamfiles_o2\" [label=\"INPUT\"];\n  \"input_bam\" -> \"picard_mergesamfiles_o2\" [label=\"OUTPUT\"];\n  \"sort_scattered_fastq_s\" -> \"decider_bwa_se\" [label=\"fastq_path\"];\n  \"bam_readgroup_to_json\" -> \"decider_bwa_se\" [label=\"readgroup_path\"];\n  \"sort_scattered_fastq_o2\" -> \"decider_bwa_o2\" [label=\"fastq_path\"];\n  \"bam_readgroup_to_json\" -> \"decider_bwa_o2\" [label=\"readgroup_path\"];\n  \"biobambam_bamtofastq\" -> \"remove_duplicate_fastq1\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"merge_fastqc_db_o1_sqlite\" [label=\"job_uuid\"];\n  \"fastqc_db_o1\" -> \"merge_fastqc_db_o1_sqlite\" [label=\"source_sqlite\"];\n  \"job_uuid\" -> \"fastqc_db2\" [label=\"job_uuid\"];\n  \"fastqc2\" -> \"fastqc_db2\" [label=\"INPUT\"];\n  \"readgroup_json_db\" -> \"merge_readgroup_json_db\" [label=\"source_sqlite\"];\n  \"job_uuid\" -> \"merge_readgroup_json_db\" [label=\"job_uuid\"];\n  \"biobambam_bamtofastq\" -> \"remove_duplicate_fastq_s\" [label=\"INPUT\"];\n  \"biobambam_bamtofastq\" -> \"remove_duplicate_fastq_o2\" [label=\"INPUT\"];\n  \"merge_fastqc_db_o2_sqlite\" -> \"fastqc_o2_basicstats_json\" [label=\"sqlite_path\"];\n  \"fastqc_o2\" -> \"fastqc_db_o2\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"fastqc_db_o2\" [label=\"job_uuid\"];\n  \"picard_sortsam_pe\" -> \"picard_mergesamfiles_pe\" [label=\"INPUT\"];\n  \"input_bam\" -> \"picard_mergesamfiles_pe\" [label=\"OUTPUT\"];\n  \"sort_scattered_fastq_s\" -> \"fastqc_s\" [label=\"INPUT\"];\n  \"thread_count\" -> \"fastqc_s\" [label=\"threads\"];\n  \"reference_sequence\" -> \"gatk_baserecalibrator\" [label=\"reference\"];\n  \"known_snp\" -> \"gatk_baserecalibrator\" [label=\"known-sites\"];\n  \"picard_markduplicates\" -> \"gatk_baserecalibrator\" [label=\"input\"];\n  \"decider_bwa_se\" -> \"bwa_se\" [label=\"readgroup_json_path\"];\n  \"sort_scattered_fastq_s\" -> \"bwa_se\" [label=\"fastq\"];\n  \"fastqc_se_basicstats_json\" -> \"bwa_se\" [label=\"fastqc_json_path\"];\n  \"reference_sequence\" -> \"bwa_se\" [label=\"fasta\"];\n  \"thread_count\" -> \"bwa_se\" [label=\"thread_count\"];\n  \"bwa_se\" -> \"picard_sortsam_se\" [label=\"INPUT\"];\n  \"decider_bwa_o2\" -> \"bwa_o2\" [label=\"readgroup_json_path\"];\n  \"thread_count\" -> \"bwa_o2\" [label=\"thread_count\"];\n  \"reference_sequence\" -> \"bwa_o2\" [label=\"fasta\"];\n  \"fastqc_o2_basicstats_json\" -> \"bwa_o2\" [label=\"fastqc_json_path\"];\n  \"sort_scattered_fastq_o2\" -> \"bwa_o2\" [label=\"fastq\"];\n  \"bwa_o2\" -> \"picard_sortsam_o2\" [label=\"INPUT\"];\n  \"bam_readgroup_to_json\" -> \"decider_bwa_pe\" [label=\"readgroup_path\"];\n  \"sort_scattered_fastq1\" -> \"decider_bwa_pe\" [label=\"fastq_path\"];\n  \"bam_reheader\" -> \"picard_markduplicates\" [label=\"INPUT\"];\n  \"thread_count\" -> \"fastqc_o2\" [label=\"threads\"];\n  \"sort_scattered_fastq_o2\" -> \"fastqc_o2\" [label=\"INPUT\"];\n  \"input_bam\" -> \"samtools_bamtobam\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"picard_validatesamfile_bqsr_to_sqlite\" [label=\"job_uuid\"];\n  \"picard_validatesamfile_bqsr\" -> \"picard_validatesamfile_bqsr_to_sqlite\" [label=\"metric_path\"];\n  \"gatk_applybqsr\" -> \"picard_validatesamfile_bqsr_to_sqlite\" [label=\"bam\"];\n  \"picard_sortsam_o1\" -> \"picard_mergesamfiles_o1\" [label=\"INPUT\"];\n  \"input_bam\" -> \"picard_mergesamfiles_o1\" [label=\"OUTPUT\"];\n  \"bwa_pe\" -> \"picard_sortsam_pe\" [label=\"INPUT\"];\n  \"sort_scattered_fastq1\" -> \"bwa_pe\" [label=\"fastq1\"];\n  \"fastqc_pe_basicstats_json\" -> \"bwa_pe\" [label=\"fastqc_json_path\"];\n  \"thread_count\" -> \"bwa_pe\" [label=\"thread_count\"];\n  \"decider_bwa_pe\" -> \"bwa_pe\" [label=\"readgroup_json_path\"];\n  \"reference_sequence\" -> \"bwa_pe\" [label=\"fasta\"];\n  \"sort_scattered_fastq2\" -> \"bwa_pe\" [label=\"fastq2\"];\n  \"merge_fastqc_db1_sqlite\" -> \"fastqc_pe_basicstats_json\" [label=\"sqlite_path\"];\n  \"remove_duplicate_fastq_o2\" -> \"sort_scattered_fastq_o2\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"merge_fastqc_db1_sqlite\" [label=\"job_uuid\"];\n  \"fastqc_db1\" -> \"merge_fastqc_db1_sqlite\" [label=\"source_sqlite\"];\n  \"bam_readgroup_to_json\" -> \"decider_bwa_o1\" [label=\"readgroup_path\"];\n  \"sort_scattered_fastq_o1\" -> \"decider_bwa_o1\" [label=\"fastq_path\"];\n  \"picard_mergesamfiles_se\" -> \"picard_mergesamfiles\" [label=\"INPUT\"];\n  \"picard_mergesamfiles_pe\" -> \"picard_mergesamfiles\" [label=\"INPUT\"];\n  \"picard_mergesamfiles_o2\" -> \"picard_mergesamfiles\" [label=\"INPUT\"];\n  \"picard_mergesamfiles_o1\" -> \"picard_mergesamfiles\" [label=\"INPUT\"];\n  \"input_bam\" -> \"picard_mergesamfiles\" [label=\"OUTPUT\"];\n  \"fastqc1\" -> \"fastqc_db1\" [label=\"INPUT\"];\n  \"job_uuid\" -> \"fastqc_db1\" [label=\"job_uuid\"];\n  \"biobambam_bamtofastq\" -> \"remove_duplicate_fastq_o1\" [label=\"INPUT\"];\n  \"fastqc_db_s\" -> \"merge_fastqc_db_s_sqlite\" [label=\"source_sqlite\"];\n  \"job_uuid\" -> \"merge_fastqc_db_s_sqlite\" [label=\"job_uuid\"];\n  \"merge_fastqc_db_s_sqlite\" -> \"fastqc_se_basicstats_json\" [label=\"sqlite_path\"];\n  \"merge_all_sqlite\" -> \"sqlite\";\n  \"gatk_applybqsr\" -> \"bam\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/1326fb7fedca91a274fb7596c9052a4d279eacf9/workflows/dnaseq/transform.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/NCI-GDC/gdc-dnaseq-cwl/blob/1326fb7fedca91a274fb7596c9052a4d279eacf9/workflows/dnaseq/transform.cwl","visualisationPng":"/graph/png/github.com/NCI-GDC/gdc-dnaseq-cwl/blob/1326fb7fedca91a274fb7596c9052a4d279eacf9/workflows/dnaseq/transform.cwl","visualisationSvg":"/graph/svg/github.com/NCI-GDC/gdc-dnaseq-cwl/blob/1326fb7fedca91a274fb7596c9052a4d279eacf9/workflows/dnaseq/transform.cwl","roBundle":"/robundle/github.com/NCI-GDC/gdc-dnaseq-cwl/blob/1326fb7fedca91a274fb7596c9052a4d279eacf9/workflows/dnaseq/transform.cwl","licenseName":"Apache License 2.0"}