--- /dev/null
+{
+ "name":"GATK / exome PE fastq to snp",
+ "components":{
+ "extract-reference":{
+ "script":"file-select",
+ "script_parameters":{
+ "names":[
+ "human_g1k_v37.fasta.gz", "human_g1k_v37.fasta.fai.gz", "human_g1k_v37.dict.gz"
+ ],
+ "input":"d237a90bae3870b3b033aea1e99de4a9+10820+K@qr1hi"
+ },
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d"
+ },
+ "bwa-index":{
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script":"bwa-index",
+ "script_parameters":{
+ "input":{
+ "output_of":"extract-reference"
+ },
+ "bwa_tbz":{
+ "optional":false
+ }
+ }
+ },
+ "bwa-aln":{
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script":"bwa-aln",
+ "script_parameters":{
+ "input":{
+ "optional":"false"
+ },
+ "reference_index":{
+ "output_of":"bwa-index"
+ },
+ "samtools_tgz":{
+ "optional":false
+ },
+ "bwa_tbz":{
+ "optional":false
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":1
+ }
+ },
+ "picard-gatk2-prep":{
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script":"picard-gatk2-prep",
+ "script_parameters":{
+ "input":{
+ "output_of":"bwa-aln"
+ },
+ "reference":{
+ "output_of":"extract-reference"
+ },
+ "picard_zip":{
+ "optional":false
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":1
+ }
+ },
+ "GATK2-realign":{
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script":"GATK2-realign",
+ "script_parameters":{
+ "input":{
+ "output_of":"picard-gatk2-prep"
+ },
+ "gatk_bundle":{
+ "optional":false
+ },
+ "picard_zip":{
+ "optional":false
+ },
+ "gatk_tbz":{
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+ },
+ "regions":{
+ "optional":true
+ },
+ "region_padding":{
+ "optional":true
+ }
+ },
+ "runtime_constraints":{
+ "max_tasks_per_node":2
+ }
+ },
+ "GATK2-bqsr":{
+ "script_version":"82a471c92036198aaf02ca0467ea48d49dbe822d",
+ "script":"GATK2-bqsr",
+ "script_parameters":{
+ "input":{
+ "output_of":"GATK2-realign"
+ },
+ "gatk_bundle":{
+ "optional":false
+ },
+ "picard_zip":{
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+ },
+ "gatk_tbz":{
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+ }
+ }
+ },
+ "GATK2-merge-call":{
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+ "script":"GATK2-merge-call",
+ "script_parameters":{
+ "input":{
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+ },
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+ },
+ "regions":{
+ "optional":true
+ },
+ "region_padding":{
+ "optional":true
+ },
+ "GATK2_UnifiedGenotyper_args":{
+ "default":["-stand_call_conf","30.0","-stand_emit_conf","30.0","-dcov","200"]
+ }
+ }
+ }
+ }
+}