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CNV Profiler WDL #69

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CNV Profiler WDL #69

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47a44af
first commit of CNV profiler
yueyaog Jul 2, 2024
c6aa0f3
added to dockstore yml
yueyaog Jul 2, 2024
7bf2094
updated the padded command
yueyaog Jul 2, 2024
7fa5bf9
update SSD disk requirement
yueyaog Jul 2, 2024
adaa808
bed file format bug fix
yueyaog Jul 3, 2024
8b2e677
bug fix
yueyaog Jul 3, 2024
b69663b
bug fix for padded section
yueyaog Jul 3, 2024
6fd175f
argument name bug fix
yueyaog Jul 3, 2024
27e3155
updated the depth viz
yueyaog Jul 22, 2024
a64c536
adjust the padding logic
yueyaog Jul 23, 2024
b2e9d27
fixed syntax error
yueyaog Jul 23, 2024
d1e43be
docker image update with output path changes
yueyaog Jul 23, 2024
bcf98a8
update WDL according to viz tool change
yueyaog Jul 31, 2024
4d53cee
bug fix wrong arg name
yueyaog Jul 31, 2024
413d9d2
acccept CNV intervals
yueyaog Sep 25, 2024
ba11915
change the create BED script from bash to python
yueyaog Sep 25, 2024
e42d569
updated create bed from interval task
yueyaog Sep 25, 2024
ee951ee
updated default docker tag
yueyaog Sep 25, 2024
a2d2ed5
update default task runtime config
yueyaog Sep 25, 2024
91e5d8f
removed CNV input validation task
yueyaog Sep 25, 2024
ab70524
Remove empty line from createBed Output
yueyaog Sep 25, 2024
061c114
updated the docker image to public repo
yueyaog Sep 25, 2024
75be1fc
resolved dockstore conflict
yueyaog Sep 27, 2024
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6 changes: 6 additions & 0 deletions .dockstore.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,11 @@ workflows:
primaryDescriptorPath: /PECGS-QUICviz/QUICviz.wdl
testParameterFiles:
- /PECGS-QUICviz/QUICviz.inputs.json
- name: CNV-Profiler
subclass: WDL
primaryDescriptorPath: /CNV-Profiler/CNV-Profiler.wdl
testParameterFiles:
- /CNV-Profiler/CNV-Profiler.inputs.json
- name: cnvArrayProber
subclass: WDL
primaryDescriptorPath: /CNV_Array_Prober/cnvArrayProber.wdl
Expand All @@ -139,3 +144,4 @@ workflows:
primaryDescriptorPath: /CallabilityAnalysis/Callability_Analysis_update.wdl
testParameterFiles:
- /CallabilityAnalysis/Callability_Analysis_update.inputs.json

37 changes: 37 additions & 0 deletions CNV-Profiler/CNV-Profiler.inputs.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
{
"CNV_Profiler.CramToBam.mem": "Int (optional, default = 64)",
"CNV_Profiler.SamtoolsDepth.cpu": "Int? (optional)",
"CNV_Profiler.GetPaddedCnvBed.mem_gb": "Int (optional, default = 1)",
"CNV_Profiler.SamtoolsDepth.disk_size_gb": "Int? (optional)",
"CNV_Profiler.cnvDepthProfiler.maxRetries": "Int (optional, default = 1)",
"CNV_Profiler.cramOrBamIndexFile": "File",
"CNV_Profiler.HeterozygosityCheck.maxRetries": "Int (optional, default = 1)",
"CNV_Profiler.HeterozygosityCheck.cpu": "Int (optional, default = 8)",
"CNV_Profiler.cramOrBamFile": "File",
"CNV_Profiler.HeterozygosityCheck.HG2_vcf_path": "File (optional, default = \"gs://dragenv4_2_validation/dragen_4_2_4/hg19/NA24385/NA24385.hard-filtered.vcf.gz\")",
"CNV_Profiler.HeterozygosityCheck.mem_gb": "Int (optional, default = 64)",
"CNV_Profiler.cnvDepthProfiler.cpu": "Int (optional, default = 8)",
"CNV_Profiler.cnvDepthProfiler.preemptible": "Int (optional, default = 0)",
"CNV_Profiler.SamtoolsDepth.minBaseQuality": "Int (optional, default = 20)",
"CNV_Profiler.heterozygosityCheck": "Boolean (optional, default = false)",
"CNV_Profiler.CramToBam.cpu": "Int (optional, default = 8)",
"CNV_Profiler.HeterozygosityCheck.disk_size_gb": "Int (optional, default = 500)",
"CNV_Profiler.hardFilteredVcfFile": "File? (optional)",
"CNV_Profiler.GetPaddedCnvBed.cpu": "Int (optional, default = 1)",
"CNV_Profiler.referenceFasta": "File",
"CNV_Profiler.GetPaddedCnvBed.disk_size_gb": "Int (optional, default = 10)",
"CNV_Profiler.cnvDepthProfiler.mem_gb": "Int (optional, default = 64)",
"CNV_Profiler.cnvDepthProfiler.disk_size_gb": "Int (optional, default = 500)",
"CNV_Profiler.sampleName": "String",
"CNV_Profiler.cnvProfiler_Docker": "String (optional, default = \"us-central1-docker.pkg.dev/tag-team-160914/gptag-dockers/covprofileviz:0.0.2\")",
"CNV_Profiler.referenceDict": "File",
"CNV_Profiler.SamtoolsDepth.samtools_docker": "String (optional, default = \"euformatics/samtools:1.20\")",
"CNV_Profiler.referenceFastaIndex": "File",
"CNV_Profiler.SamtoolsDepth.minMappingQuality": "Int (optional, default = 20)",
"CNV_Profiler.HeterozygosityCheck.HG1_vcf_path": "File (optional, default = \"gs://dragenv4_2_validation/dragen_4_2_4/hg19/NA12878/smoke.hard-filtered.vcf.gz\")",
"CNV_Profiler.SamtoolsDepth.mem_gb": "Int? (optional)",
"CNV_Profiler.CramToBam.disk_size": "Int (optional, default = 500)",
"CNV_Profiler.HeterozygosityCheck.preemptible": "Int (optional, default = 0)",
"CNV_Profiler.cnvBedFile": "File"
}

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