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Rudimentary support for other output types, support for scattering ex…
…tract cohort (#6949) * cohort extract work for WGS * rudimentary support for configurable output types * support for nocalls * extract wdl, missing classes, and compiler warning * tidying
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,13 @@ | ||
| { | ||
| "NgsCohortExtract.reference": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta", | ||
| "NgsCohortExtract.reference_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai", | ||
| "NgsCohortExtract.reference_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict", | ||
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| "NgsCohortExtract.gatk_override": "gs://broad-dsp-spec-ops/kcibul/gatk-package-4.1.8.1-140-g8aa14d3-SNAPSHOT-local.jar", | ||
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| "NgsCohortExtract.fq_sample_table": "spec-ops-aou.kc_high_cov_ccdg.cohort_100_of_194", | ||
| "NgsCohortExtract.fq_cohort_extract_table": "spec-ops-aou.kc_high_cov_ccdg.exported_cohort_100_test", | ||
| "NgsCohortExtract.query_project": "spec-ops-aou", | ||
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| "NgsCohortExtract.output_file_base_name": "ccdg_high_cov_export_100" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,115 @@ | ||
| version 1.0 | ||
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| workflow NgsCohortExtract { | ||
| input { | ||
| Int max_chrom_id = 24 | ||
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| # bug in cromwell, can't support large integers... | ||
| # https://github.com/broadinstitute/cromwell/issues/2685 | ||
| String chrom_offset = "1000000000000" | ||
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| File reference | ||
| File reference_index | ||
| File reference_dict | ||
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| String fq_sample_table | ||
| String fq_cohort_extract_table | ||
| String query_project | ||
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| String output_file_base_name | ||
| File? gatk_override | ||
| } | ||
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| scatter(i in range(max_chrom_id)) { | ||
| call ExtractTask { | ||
| input: | ||
| gatk_override = gatk_override, | ||
| reference = reference, | ||
| reference_index = reference_index, | ||
| reference_dict = reference_dict, | ||
| fq_sample_table = fq_sample_table, | ||
| chrom_offset = chrom_offset, | ||
| chrom_id = i+1, | ||
| fq_cohort_extract_table = fq_cohort_extract_table, | ||
| read_project_id = query_project, | ||
| output_file = "${output_file_base_name}_${i}.vcf.gz" | ||
| } | ||
| } | ||
| } | ||
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| ################################################################################ | ||
| task ExtractTask { | ||
| # indicates that this task should NOT be call cached | ||
| meta { | ||
| volatile: true | ||
| } | ||
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| input { | ||
| # ------------------------------------------------ | ||
| # Input args: | ||
| File reference | ||
| File reference_index | ||
| File reference_dict | ||
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| String fq_sample_table | ||
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| # bug in cromwell, can't support large integers... | ||
| # https://github.com/broadinstitute/cromwell/issues/2685 | ||
| String chrom_offset | ||
| Int chrom_id | ||
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| String fq_cohort_extract_table | ||
| String read_project_id | ||
| String output_file | ||
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| # Runtime Options: | ||
| File? gatk_override | ||
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| Int? local_sort_max_records_in_ram = 10000000 | ||
| } | ||
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| # ------------------------------------------------ | ||
| # Run our command: | ||
| command <<< | ||
| set -e | ||
| export GATK_LOCAL_JAR=~{default="/root/gatk.jar" gatk_override} | ||
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| df -h | ||
| min_location=$(echo "~{chrom_id} * ~{chrom_offset}" | bc) | ||
| max_location=$(echo "( ~{chrom_id} + 1 ) * ~{chrom_offset}" | bc) | ||
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| gatk --java-options "-Xmx4g" \ | ||
| ExtractCohort \ | ||
| --mode GENOMES --ref-version 38 --query-mode LOCAL_SORT \ | ||
| -R "~{reference}" \ | ||
| -O "~{output_file}" \ | ||
| --local-sort-max-records-in-ram ~{local_sort_max_records_in_ram} \ | ||
| --sample-table ~{fq_sample_table} \ | ||
| --cohort-extract-table ~{fq_cohort_extract_table} \ | ||
| --min-location ${min_location} --max-location ${max_location} \ | ||
| --project-id ~{read_project_id} | ||
| >>> | ||
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| # ------------------------------------------------ | ||
| # Runtime settings: | ||
| runtime { | ||
| docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_d8a72b825eab2d979c8877448c0ca948fd9b34c7_change_to_hwe" | ||
| memory: "7 GB" | ||
| disks: "local-disk 10 HDD" | ||
| bootDiskSizeGb: 15 | ||
| preemptible: 3 | ||
| cpu: 2 | ||
| } | ||
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| # ------------------------------------------------ | ||
| # Outputs: | ||
| output { | ||
| File output_vcf = "~{output_file}" | ||
| File output_vcf_index = "~{output_file}.tbi" | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
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@@ -197,4 +197,10 @@ public enum ModeEnum { | |
| GENOMES, | ||
| ARRAYS | ||
| } | ||
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| public enum OutputType { | ||
| TSV, | ||
| ORC, | ||
| PARQUET | ||
| } | ||
| } | ||
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