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Hangsu phasing #417

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Hangsu phasing #417

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1476b01
new branch for whatshapPhasing and Shapeit5
hangsuUNC Aug 16, 2023
c6d906a
revise Shapeit5 wdl by adding scaffold info
hangsuUNC Aug 16, 2023
41d0a11
revise: --tag=PS
hangsuUNC Aug 18, 2023
df94407
integrate whatshap shapeit4 and shapeit5
hangsuUNC Aug 18, 2023
825246a
change tbi to sci
hangsuUNC Aug 19, 2023
e26b47f
add workflow for drawing graph using Bandage
hangsuUNC Nov 13, 2023
944800c
add docker files
hangsuUNC Nov 13, 2023
c549bbc
modify dockstore
hangsuUNC Nov 13, 2023
07017ef
add files
hangsuUNC Jan 19, 2024
0fd86f5
revise sort
hangsuUNC Jan 19, 2024
ec37197
add merge phased vcfs
hangsuUNC Jan 22, 2024
6479a4b
revise MergePhasedVCF
hangsuUNC Jan 22, 2024
602eb21
revise description
hangsuUNC Jan 22, 2024
e653658
add preprocessing
hangsuUNC Jan 22, 2024
a38d1ae
add prefix
hangsuUNC Jan 22, 2024
78d6e67
ConvertHailMT
hangsuUNC Jan 22, 2024
ef8916b
revise parameter
hangsuUNC Jan 22, 2024
0502c3d
ConvertToHailMTT2T
hangsuUNC Jan 22, 2024
b741fb1
revise CollectionDefinitions
hangsuUNC Jan 22, 2024
a5ab9b4
revise CollectionDefinition
hangsuUNC Jan 22, 2024
7d5c017
convert to hail mt
hangsuUNC Jan 22, 2024
2ed83f4
ConvertToHailMTT2T
hangsuUNC Jan 22, 2024
693097f
ConvertToHail
hangsuUNC Jan 23, 2024
74af3a1
revise reference name
hangsuUNC Jan 23, 2024
56761de
fds
hangsuUNC Jan 23, 2024
f3cc4e3
revise disk size
hangsuUNC Jan 23, 2024
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revise MergePhasedVCF
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@hangsuUNC
hangsuUNC committed Jan 22, 2024
commit 6479a4b9fb5a9c897460bb6d2f0cf67d999fa5dd
7 changes: 6 additions & 1 deletion wdl/pipelines/PacBio/Utility/MergePhasedVCF.wdl
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Expand Up @@ -12,11 +12,16 @@ workflow MergePhasedVCF{
File reference_fasta_fai
}
call FindFiles{input: sampleFolder = SampleFolder}
call VU.CollectDefinitions as CD {
input:
vcfs = FindFiles.vcfFiles
}
call VU.MergeAndSortVCFs as Merge {
input:
vcfs = FindFiles.vcfFiles,
ref_fasta_fai = reference_fasta_fai,
prefix = Samplename
prefix = Samplename,
header_definitions_file = CD.union_definitions
}

output{
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