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Dev #30

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Jan 13, 2020
Merged

Dev #30

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d1c5cbc
README.md
Nov 7, 2018
4b08f6a
Update to gatk4.1
Feb 1, 2019
ab1fccc
Updated forum links in Readme
Feb 1, 2019
f2ec9cc
changed ref file VM path to google bucket path
Feb 1, 2019
ad695aa
Merge branch 'master' into dev
Feb 1, 2019
257166f
updated import link to git tag url
Feb 1, 2019
9b0c86f
Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs…
Apr 2, 2019
b814bc3
updated to GATK4.1.1.0
Apr 2, 2019
579e36a
minor edits
Apr 2, 2019
f722ae4
changed import to dev for pon
Apr 2, 2019
1594883
updated filter bias variable
Apr 4, 2019
6f58280
updated filter bias variable
Apr 4, 2019
92c1abf
updated output variable names, removed artifact_mode from normal-normal
Apr 4, 2019
0f38435
changed index to idx
Apr 4, 2019
5da3b20
removed artifact_modes
Apr 4, 2019
0ecee17
updated import to next release: 2.4.0
Apr 5, 2019
1719562
specified gatk version in readme
Apr 5, 2019
566fec1
Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs…
Apr 25, 2019
f055dfc
Added Funcotator note to readme
Apr 25, 2019
0d31a9f
Update to gatk4.1.2.0
Apr 25, 2019
de2d5b3
updated input variable for mutect2
Apr 25, 2019
4054e9b
correctin to input vairalbe
Apr 25, 2019
d7438e1
correction to output variable
Apr 25, 2019
7e22a33
corrected variable name and simplified json
Aug 19, 2019
1494e0b
Merge branch 'master' into dev
Aug 19, 2019
1026dbe
Merge branch 'master' of github.com:gatk-workflows/gatk4-somatic-snvs…
Sep 23, 2019
7dabf3c
renamed input json, removed optional variables from json, updated reg…
Sep 23, 2019
8b690cb
removed nio wdl
Sep 23, 2019
6c8374d
minor update
Sep 23, 2019
9bc5597
Merge branch 'dev' of github.com:gatk-workflows/gatk4-somatic-snvs-in…
Sep 23, 2019
17af7dd
removed comments in json because later version of cromwell throws err…
Sep 23, 2019
0a5b6bd
corrections to import url for pon wdl
Sep 23, 2019
356a43d
mutect2 WDL and pon WDL had inconsistent input names
Sep 26, 2019
98316f3
mutect2 WDL and pon WDL had inconsistent input names
Sep 26, 2019
694372a
added standard_runtime to pon
Sep 26, 2019
c816321
add runtime structs
Sep 26, 2019
085ea22
add runtime structs for mergevcf
Sep 26, 2019
7cfd447
Update mutect2_pon.wdl
Sep 27, 2019
af9cacc
cleaned up input variables
Sep 30, 2019
dc46cd8
Update README.md
Sep 30, 2019
00328d1
updated docker to 4.1.4.0, updated import url to latest release
Oct 11, 2019
bb1c6b2
Merge branch 'dev' of github.com:gatk-workflows/gatk4-somatic-snvs-in…
Oct 11, 2019
f503d0b
updated docker to 4.1.4.1, updated mutect.wdl to 4.1.4.1 gatk release
Jan 2, 2020
6910f24
Merge branch 'master' into dev
Jan 3, 2020
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updated output variable names, removed artifact_mode from normal-normal
  • Loading branch information
bshifaw committed Apr 4, 2019
commit 92c1abff7f120e9b0cf0078dc33556b1c32da8ec
5 changes: 2 additions & 3 deletions mutect2-normal-normal.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -72,7 +72,6 @@ workflow Mutect2NormalNormal {
variants_for_contamination = variants_for_contamination,
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 +87,7 @@ 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 +99,7 @@ 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)
}
}

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8 changes: 4 additions & 4 deletions mutect2_pon.wdl
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Expand Up @@ -44,8 +44,8 @@ workflow Mutect2_Panel {
ref_fasta = ref_fasta,
ref_fai = ref_fai,
ref_dict = ref_dict,
tumor_bam = normal_bam.left,
tumor_bai = normal_bam.right,
tumor_reads = normal_bam.left,
tumor_reads_index = normal_bam.right,
scatter_count = scatter_count,
m2_extra_args = select_first([m2_extra_args, ""]) + "--max-mnp-distance 0",
gatk_override = gatk_override,
Expand Down Expand Up @@ -99,9 +99,9 @@ workflow Mutect2_Panel {

output {
File pon = MergeVCFs.merged_vcf
File pon_idx = MergeVCFs.merged_vcf_index
File pon_idx = MergeVCFs.merged_vcf_idx
Array[File] normal_calls = Mutect2.filtered_vcf
Array[File] normal_calls_idx = Mutect2.filtered_vcf_index
Array[File] normal_calls_idx = Mutect2.filtered_vcf_idx
}
}

Expand Down