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Wdlupdate (#9)
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* Update to gatk4.0.8.1 release

* added link to 'How to run workflow' document
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bshifaw authored Aug 17, 2018
1 parent 0ab43b7 commit ee683a7
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4 changes: 4 additions & 0 deletions README.md
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Expand Up @@ -83,3 +83,7 @@ Cromwell version support
override:NCBI_Build=37,Strand=+,status=Somatic,phase=Phase_I,sequencer=Illumina,Tumor_Validation_Allele1=,Tumor_Validation_Allele2=,Match_Norm_Validation_Allele1=,Match_Norm_Validation_Allele2=,Verification_Status=,Validation_Status=,Validation_Method=,Score=,BAM_file=,Match_Norm_Seq_Allele1=,Match_Norm_Seq_Allele2=
```

### Important Note :
- Runtime parameters are optimized for Broad's Google Cloud Platform implementation.
- For help running workflows on the Google Cloud Platform or locally please
view the following tutorial [(How to) Execute Workflows from the gatk-workflows Git Organization](https://software.broadinstitute.org/gatk/documentation/article?id=12521)
2 changes: 1 addition & 1 deletion mutect2-normal-normal.inputs.json
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Expand Up @@ -34,6 +34,6 @@
"Mutect2NormalNormal.scatter_count": "10",

"##_COMMENT4": "Docker",
"Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.0.5.0"
"Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.0.8.1"
}

2 changes: 1 addition & 1 deletion mutect2.exome.inputs.json
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@@ -1,7 +1,7 @@
{
"##_COMMENT1": "Runtime",
"##Mutect2.oncotator_docker": "(optional) String?",
"Mutect2.gatk_docker": "broadinstitute/gatk:4.0.5.0",
"Mutect2.gatk_docker": "broadinstitute/gatk:4.0.8.1",

"##_COMMENT2": "Workflow options",
"Mutect2.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
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467 changes: 339 additions & 128 deletions mutect2.wdl
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319 changes: 196 additions & 123 deletions mutect2_nio.wdl
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69 changes: 34 additions & 35 deletions mutect2_pon.inputs.json
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Expand Up @@ -3,23 +3,22 @@
"Mutect2_Panel.normal_bams": "Array[File]",
"Mutect2_Panel.normal_bais": "Array[File]",
"Mutect2_Panel.pon_name": "String",
"##_Mutect2_Panel.Mutect2.normal_bam": "(optional) File?",
"##_Mutect2_Panel.Mutect2.normal_bai": "(optional) File?",

"#Mutect2_Panel.Mutect2.normal_bam": "(optional) File?",
"#Mutect2_Panel.Mutect2.normal_bai": "(optional) File?",

"##_COMMENT2": "Primary resources",
"Mutect2_Panel.ref_fasta": "File",
"Mutect2_Panel.ref_fai": "File",
"Mutect2_Panel.ref_dict": "File",
"Mutect2_Panel.scatter_count": "Int",
"Mutect2_Panel.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
"Mutect2_Panel.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
"Mutect2_Panel.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",
"Mutect2_Panel.scatter_count": "10",

"##_COMMENT3": "Secondary resources",
"##_Mutect2_Panel.intervals": "(optional) File?",
"Mutect2_Panel.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
"##_Mutect2_Panel.Mutect2.data_sources_tar_gz": "(optional) String?",
"##_Mutect2_Panel.Mutect2.variants_for_contamination": "(optional) File?",
"Mutect2_Panel.Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
"##_Mutect2_Panel.Mutect2.variants_for_contamination_index": "(optional) File?",
"##_Mutect2_Panel.Mutect2.tumor_sequencing_artifact_metrics": "(optional) File?",
"##_Mutect2_Panel.Mutect2.gnomad": "(optional) File?",
"Mutect2_Panel.Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",
"##_Mutect2_Panel.Mutect2.gnomad_index": "(optional) File?",
"##_Mutect2_Panel.Mutect2.onco_ds_tar_gz": "(optional) File?",
"##_Mutect2_Panel.Mutect2.pon": "(optional) File?",
Expand All @@ -28,39 +27,39 @@
"##_Mutect2_Panel.gatk_override": "(optional) File?",

"##_COMMENT4": "Secondary resources",
"##_Mutect2_Panel.duplicate_sample_strategy": "(optional) String?",
"##_Mutect2_Panel.m2_extra_args": "(optional) String?",
"##_Mutect2_Panel.Mutect2.onco_ds_local_db_dir": "(optional) String?",
"##_Mutect2_Panel.Mutect2.annotation_defaults": "(optional) Array[String]?",
"##_Mutect2_Panel.Mutect2.reference_version": "(optional) String?",
"##_Mutect2_Panel.Mutect2.annotation_overrides": "(optional) Array[String]?",
"##_Mutect2_Panel.Mutect2.artifact_modes": "(optional) Array[String]?",
"##_Mutect2_Panel.Mutect2.sequence_source": "(optional) String?",
"##_Mutect2_Panel.Mutect2.transcript_selection_list": "(optional) Array[String]?",
"##_Mutect2_Panel.Mutect2.split_intervals_extra_args": "(optional) String?",
"##_Mutect2_Panel.Mutect2.sequencing_center": "(optional) String?",
"##_Mutect2_Panel.Mutect2.transcript_selection_mode": "(optional) String?",
"##_Mutect2_Panel.Mutect2.m2_extra_filtering_args": "(optional) String?",
"#Mutect2_Panel.duplicate_sample_strategy": "(optional) String?",
"#Mutect2_Panel.m2_extra_args": "(optional) String?",
"#Mutect2_Panel.Mutect2.onco_ds_local_db_dir": "(optional) String?",
"#Mutect2_Panel.Mutect2.annotation_defaults": "(optional) Array[String]?",
"#Mutect2_Panel.Mutect2.reference_version": "(optional) String?",
"#Mutect2_Panel.Mutect2.annotation_oventerrides": "(optional) Array[String]?",
"Mutect2_Panel.Mutect2.artifact_modes": ["G/T", "C/T"],
"#Mutect2_Panel.Mutect2.sequence_source": "(optional) String?",
"#Mutect2_Panel.Mutect2.transcript_selection_list": "(optional) Array[String]?",
"#Mutect2_Panel.Mutect2.split_intervals_extra_args": "(optional) String?",
"#Mutect2_Panel.Mutect2.sequencing_center": "(optional) String?",
"#Mutect2_Panel.Mutect2.transcript_selection_mode": "(optional) String?",
"#Mutect2_Panel.Mutect2.m2_extra_filtering_args": "(optional) String?",

"##_COMMENT5": "Boolean Options",
"##_Mutect2_Panel.Mutect2.run_oncotator": "(optional) Boolean?",
"##_Mutect2_Panel.Mutect2.make_bamout": "(optional) Boolean?",
"##_Mutect2_Panel.Mutect2.run_funcotator": "(optional) Boolean?",
"##_Mutect2_Panel.Mutect2.compress_vcfs": "(optional) Boolean?",
"##_Mutect2_Panel.Mutect2.run_orientation_bias_filter": "(optional) Boolean?",
"#Mutect2_Panel.Mutect2.run_oncotator": "(optional) Boolean?",
"#Mutect2_Panel.Mutect2.make_bamout": "(optional) Boolean?",
"#Mutect2_Panel.Mutect2.run_funcotator": "(optional) Boolean?",
"#Mutect2_Panel.Mutect2.compress_vcfs": "(optional) Boolean?",
"#Mutect2_Panel.Mutect2.run_orientation_bias_filter": "(optional) Boolean?",

"##_COMMENT6": "Docker",
"Mutect2_Panel.gatk_docker": "String",
"##_Mutect2_Panel.Mutect2.oncotator_docker": "(optional) String?",
"Mutect2_Panel.gatk_docker": "broadinstitute/gatk:4.0.8.1",
"#Mutect2_Panel.Mutect2.oncotator_docker": "(optional) String?",

"##_COMMENT7": "Disk space",
"##_Mutect2_Panel.Mutect2.emergency_extra_disk": "(optional) Int?",
"##_Mutect2_Panel.CreatePanel.disk_space": "(optional) Int?",
"#Mutect2_Panel.Mutect2.emergency_extra_disk": "(optional) Int?",
"#Mutect2_Panel.CreatePanel.disk_space": "(optional) Int?",

"##_COMMENT8": "Preemptibles",
"##_Mutect2_Panel.preemptible_attempts": "(optional) Int?",
"#Mutect2_Panel.preemptible_attempts": "(optional) Int?",

"##_COMMENT9": "Addtional Runtime Parameters",
"##_Mutect2_Panel.CreatePanel.mem": "(optional) Int?",
"##_Mutect2_Panel.CreatePanel.cpu": "(optional) Int?"
"#Mutect2_Panel.CreatePanel.mem": "(optional) Int?",
"#Mutect2_Panel.CreatePanel.cpu": "(optional) Int?"
}
15 changes: 10 additions & 5 deletions mutect2_pon.wdl
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Expand Up @@ -34,6 +34,7 @@ workflow Mutect2_Panel {
# runtime
String gatk_docker
Int? preemptible_attempts
Int? max_retries

Array[Pair[File,File]] normal_bam_pairs = zip(normal_bams, normal_bais)

Expand All @@ -53,26 +54,28 @@ workflow Mutect2_Panel {
m2_extra_args = m2_extra_args,
gatk_override = gatk_override,
gatk_docker = gatk_docker,
preemptible_attempts = preemptible_attempts
preemptible_attempts = preemptible_attempts,
max_retries = max_retries
}
}

call CreatePanel {
input:
input_vcfs = Mutect2.unfiltered_vcf,
input_vcfs_idx = Mutect2.unfiltered_vcf_index,
input_vcfs = Mutect2.filtered_vcf,
input_vcfs_idx = Mutect2.filtered_vcf_index,
duplicate_sample_strategy = duplicate_sample_strategy,
output_vcf_name = pon_name,
gatk_override = gatk_override,
preemptible_attempts = preemptible_attempts,
max_retries = max_retries,
gatk_docker = gatk_docker
}

output {
File pon = CreatePanel.output_vcf
File pon_idx = CreatePanel.output_vcf_index
Array[File] normal_calls = Mutect2.unfiltered_vcf
Array[File] normal_calls_idx = Mutect2.unfiltered_vcf_index
Array[File] normal_calls = Mutect2.filtered_vcf
Array[File] normal_calls_idx = Mutect2.filtered_vcf_index
}
}

Expand All @@ -89,6 +92,7 @@ task CreatePanel {
String gatk_docker
Int? mem
Int? preemptible_attempts
Int? max_retries
Int? disk_space
Int? cpu
Boolean use_ssd = false
Expand All @@ -108,6 +112,7 @@ task CreatePanel {
memory: machine_mem + " GB"
disks: "local-disk " + select_first([disk_space, 100]) + if use_ssd then " SSD" else " HDD"
preemptible: select_first([preemptible_attempts, 3])
maxRetries: select_first([max_retries, 0])
cpu: select_first([cpu, 1])
}

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