Skip to content
This repository has been archived by the owner on Jul 21, 2020. It is now read-only.

Commit

Permalink
Dev (#17)
Browse files Browse the repository at this point in the history 
* updated to GATK4.1.1.0

* minor edits

* changed import to dev for pon

* updated filter bias variable

* updated output variable names, removed artifact_mode from normal-normal

* changed index to idx

* removed artifact_modes

* updated import to next release: 2.4.0
  • Loading branch information
bshifaw authored Apr 5, 2019
1 parent 3b2a121 commit 24a12ff
Show file tree
Hide file tree
Showing 7 changed files with 760 additions and 657 deletions.
2 changes: 1 addition & 1 deletion mutect2-normal-normal.inputs.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,6 @@
"Mutect2NormalNormal.scatter_count": "10",

"##_COMMENT4": "Docker",
"Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.0.8.1"
"Mutect2NormalNormal.gatk_docker": "broadinstitute/gatk:4.1.1.0"
}

40 changes: 19 additions & 21 deletions mutect2-normal-normal.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
## - False Positive VCF files and its index with summary
##
## Cromwell version support
## - Successfully tested on v30
## - Successfully tested on v36
##
## LICENSING :
## This script is released under the WDL source code license (BSD-3) (see LICENSE in
Expand All @@ -21,7 +21,7 @@
## pages at https://hub.docker.com/r/broadinstitute/* for detailed licensing information
## pertaining to the included programs.
import "https://raw.githubusercontent.com/gatk-workflows/gatk4-somatic-snvs-indels/2.3.0/mutect2_nio.wdl" as m2
import "https://raw.githubusercontent.com/gatk-workflows/gatk4-somatic-snvs-indels/2.4.0/mutect2_nio.wdl" as m2

workflow Mutect2NormalNormal {
File? intervals
Expand All @@ -34,26 +34,25 @@ workflow Mutect2NormalNormal {
File? pon
File? gnomad
File? variants_for_contamination
Boolean? run_orientation_bias_filter
Array[String]? artifact_modes
Boolean? run_orientation_bias_mixture_model_filter
File? realignment_index_bundle
String? realignment_extra_args
String? realignment_extra_args
String? m2_extra_args
String? m2_extra_filtering_args
Boolean? make_bamout
String? m2_extra_filtering_args
Boolean? make_bamout

File? gatk_override
String gatk_docker
Int? preemptible_attempts
File? gatk_override
String gatk_docker
Int? preemptible_attempts

Array[Pair[File,File]] bam_pairs = cross(bams, bams)
Array[Pair[File,File]] bai_pairs = cross(bais, bais)
Array[Pair[File,File]] bam_pairs = cross(bams, bams)
Array[Pair[File,File]] bai_pairs = cross(bais, bais)

scatter(n in range(length(bam_pairs))) {
File tumor_bam = bam_pairs[n].left
File normal_bam = bam_pairs[n].right
File tumor_bai = bai_pairs[n].left
File normal_bai = bai_pairs[n].right
File normal_bai = bai_pairs[n].right

if (tumor_bam != normal_bam) {
call m2.Mutect2 {
Expand All @@ -62,17 +61,16 @@ workflow Mutect2NormalNormal {
ref_fasta = ref_fasta,
ref_fai = ref_fai,
ref_dict = ref_dict,
tumor_bam = tumor_bam,
tumor_bai = tumor_bai,
normal_bam = normal_bam,
normal_bai = normal_bai,
tumor_reads = tumor_bam,
tumor_reads_index = tumor_bai,
normal_reads = normal_bam,
normal_reads_index = normal_bai,
pon = pon,
scatter_count = scatter_count,
gnomad = gnomad,
variants_for_contamination = variants_for_contamination,
run_orientation_bias_filter = run_orientation_bias_filter,
run_orientation_bias_mixture_model_filter = run_orientation_bias_mixture_model_filter,
preemptible_attempts = preemptible_attempts,
artifact_modes = artifact_modes,
realignment_index_bundle = realignment_index_bundle,
realignment_extra_args = realignment_extra_args,
m2_extra_args = m2_extra_args,
Expand All @@ -88,7 +86,7 @@ workflow Mutect2NormalNormal {
ref_fai = ref_fai,
ref_dict = ref_dict,
filtered_vcf = Mutect2.filtered_vcf,
filtered_vcf_index = Mutect2.filtered_vcf_index,
filtered_vcf_index = Mutect2.filtered_vcf_idx,
gatk_override = gatk_override,
gatk_docker = gatk_docker
}
Expand All @@ -100,7 +98,7 @@ workflow Mutect2NormalNormal {
output {
File summary = GatherTables.summary
Array[File] false_positives_vcfs = select_all(Mutect2.filtered_vcf)
Array[File] false_positives_vcf_indices = select_all(Mutect2.filtered_vcf_index)
Array[File] false_positives_vcf_indices = select_all(Mutect2.filtered_vcf_idx)
}
}

Expand Down
16 changes: 8 additions & 8 deletions mutect2.exome.inputs.json
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
{
"##_COMMENT1": "Runtime",
"##Mutect2.oncotator_docker": "(optional) String?",
"Mutect2.gatk_docker": "broadinstitute/gatk:4.1.0.0",
"Mutect2.gatk_docker": "broadinstitute/gatk:4.1.1.0",

"##_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",
Expand All @@ -16,18 +16,18 @@
"Mutect2.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
"Mutect2.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",
"Mutect2.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
"Mutect2.normal_bam": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
"Mutect2.normal_bai": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
"Mutect2.tumor_bam": "gs://gatk-best-practices/somatic-b37/HCC1143.bam",
"Mutect2.tumor_bai": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",
"Mutect2.normal_reads": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bam",
"Mutect2.normal_reads_index": "gs://gatk-best-practices/somatic-b37/HCC1143_normal.bai",
"Mutect2.tumor_reads": "gs://gatk-best-practices/somatic-b37/HCC1143.bam",
"Mutect2.tumor_reads_index": "gs://gatk-best-practices/somatic-b37/HCC1143.bai",

"##_COMMENT4": "Primary resources",
"Mutect2.pon": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf",
"Mutect2.pon_index": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf.idx",
"Mutect2.pon_idx": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf.idx",
"Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",
"Mutect2.gnomad_index": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx",
"Mutect2.gnomad_idx": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx",
"Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
"Mutect2.variants_for_contamination_index": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx",
"Mutect2.variants_for_contamination_idx": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx",
"##Mutect2.realignment_index_bundle": "File? (optional)",

"##_COMMENT5": "Secondary resources",
Expand Down
Loading

0 comments on commit 24a12ff

Please sign in to comment.