CrosscheckFP WDL #60
CrosscheckFP WDL #60
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@yueyaog I made some suggestions for this code. The two major points are changing the inputs to an array to allow for more than 2 samples to be cross-checked at once and including an option for not failing the workflow if the samples don't match.
| String output_name | ||
| String picard_docker = "us.gcr.io/broad-gotc-prod/genomes-in-the-cloud:2.4.1-1540490856" | ||
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| Int mismatch_rc = if fail_on_mismatch then 1 else 2 |
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| workflow CrosscheckFingerprintsWorkflow { | ||
| input { | ||
| File input_bamA |
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| File input_bamA |
| workflow CrosscheckFingerprintsWorkflow { | ||
| input { | ||
| File input_bamA | ||
| File input_bamB |
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| File input_bamB | |
| Array[File] input_bams |
| File input_bamB | ||
| File hapmap | ||
| File reference_fasta | ||
| String output_name |
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| String output_name | |
| String output_name | |
| Boolean fail_on_mismatch = false |
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| call CrosscheckFingerprints { | ||
| input: | ||
| input_bamA = input_bamA, |
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| input_bamA = input_bamA, |
| I=~{input_bamB} \ | ||
| HAPLOTYPE_MAP=~{hapmap} \ | ||
| CROSSCHECK_BY=SAMPLE \ | ||
| O=~{output_name}.crosscheck_metrics \ |
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| O=~{output_name}.crosscheck_metrics \ | |
| O=~{output_name}.crosscheck_metrics.txt \ |
| HAPLOTYPE_MAP=~{hapmap} \ | ||
| CROSSCHECK_BY=SAMPLE \ | ||
| O=~{output_name}.crosscheck_metrics \ | ||
| REFERENCE_SEQUENCE=~{reference} \ |
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| REFERENCE_SEQUENCE=~{reference} \ | |
| REFERENCE_SEQUENCE=~{reference} \ | |
| EXIT_CODE_WHEN_MISMATCH=~{mismatch_rc} \ | |
| ~{extra_args} \ |
| } | ||
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| output { | ||
| File crosscheckmetrics = "~{output_name}.crosscheck_metrics" |
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| File crosscheckmetrics = "~{output_name}.crosscheck_metrics" | |
| File crosscheckmetrics = "~{output_name}.crosscheck_metrics.txt" | |
| String crosscheck_results = if read_int("rc") == 0 then "PASS" else "FAIL" |
| File crosscheckmetrics = "~{output_name}.crosscheck_metrics" | ||
| } | ||
| } | ||
| # |
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Can you remove the commented out task here?
| output_name = output_name, | ||
| picard_docker = picard_docker | ||
| } | ||
| # call FingerprintsResult { |
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Can you remove the commented out call here?
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| runtime { | ||
| docker: picard_docker | ||
| disks: "local-disk " + disk_gb + " HDD" |
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| disks: "local-disk " + disk_gb + " HDD" | |
| disks: "local-disk " + disk_gb + " HDD" | |
| continueOnReturnCode: [0, 2] |
@MicahR-Y Here is the original crosscheck FP WDL. Feel free to suggest changes or send me the updated version you have.