2.0 - #1021

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gongyixiao wants to merge 490 commits into

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Commits on Mar 31, 2022

clean up reference config file
anoronh4
committed
0b45dd6
bugfix in reference location for travis
anoronh4
committed
8c433fb
bugfix
anoronh4
committed
6c0283d
bugfix
anoronh4
committed
405cb6a

Commits on Apr 1, 2022

Merge pull request #944 from mskcc/dsl2/feature/HRDetect
anoronh4
authored
b281444
resolve conflicts
anoronh4
committed
fd83add
revert svtools version so that it still includes AnnotSV install
anoronh4
committed
f0a7fad
fix inconsistent spacing
anoronh4
committed
fc3e4b2
Merge pull request #959 from mskcc/bugfix/Germline_maf_publishDir
gongyixiao
authored
7f0aefe
Merge pull request #962 from mskcc/bugfix/maxRetry_with_errorStrategy
gongyixiao
authored
d2adf28
catch up germline SV pipeline to the somatic SV pipeline
anoronh4
committed
cb6104e
update tag strings, publishDir paths
anoronh4
committed
1b516d6
replace deprecated 'create' channel factory with 'empty' channel factory
anoronh4
committed
2137929
bugfixes
anoronh4
committed
124a79f
fix cardinality input mismatch
anoronh4
committed
078e89c

Commits on Apr 2, 2022

bugfixes
anoronh4
committed
bf13e24

Commits on Apr 4, 2022

Commits on Apr 5, 2022

Commits on Apr 13, 2022

finetune retained vcf merge records based on number of supporting callers, to minimize spurious records
anoronh4
committed
2b89bbe

Commits on Apr 18, 2022

Lower filter threshold for Delly calls to .05
anoronh4
committed
112f3d5

Commits on Apr 26, 2022

cleaned up old unused files
anoronh4
committed
1ab81bb

Commits on May 6, 2022

Commits on Jun 22, 2022

Commits on Jun 23, 2022

Commits on Jun 24, 2022

Commits on Jun 27, 2022

bugfixes
anoronh4
committed
08b8b71
replace nan values with '.' for bedpe scripts
anoronh4
committed
cb782fc
bugfix of file name for germline annotation
anoronh4
committed
15471ad
reorganized filter_regions_bedpe.py to be more modularized
anoronh4
committed
0fe72b7
cleanup filter_regions_bedpe.py
anoronh4
committed
94e263c
add notes
anoronh4
committed
8f54439

Commits on Jun 28, 2022

Commits on Jun 29, 2022

Commits on Jun 30, 2022

bugfix for GermlineAnnotateSVBedpe inputs
anoronh4
committed
de24309
add reference for trasposable element filtering in SV
anoronh4
committed
7095a23

Commits on Jul 2, 2022

Commits on Jul 5, 2022

bugfixes
anoronh4
committed
402e7e7
fix header of bedpe due to improper handling in svtools
anoronh4
committed
194e724
bugfixes
anoronh4
committed
58f771e
remove sorting from groupTuple because elements are not ordered the same way. not sorting the groupTuple emit will not invalidate the cache, supposedly.
anoronh4
committed
3ffd2f1
fix bedpe header
anoronh4
committed
db76413
parallelize iannotatesv
anoronh4
committed
1677f13

Commits on Jul 6, 2022

bugfix
anoronh4
committed
c9c89e2
add resource configuration for *AnnotateSVBedpe processes
anoronh4
committed
d2deab4

Commits on Jul 11, 2022

Commits on Jul 15, 2022

replace empty fields in vcf with "." to prevent errors with bcftools
anoronh4
committed
bfa5fd9

Commits on Jul 22, 2022

Commits on Jul 25, 2022

Commits on Jul 26, 2022

bugfix for properly formatting insertions and deletions to match HRDetect expectations
anoronh4
committed
9541c2a

Commits on Aug 1, 2022

bugfix -- not indexing raw mergesvvcf output because it is not indexable
anoronh4
committed
1e1335e

Commits on Aug 31, 2022

Merge pull request #948 from mskcc/dsl2/feature/addFacetsBaseImg
anoronh4
authored
7c1394f

Commits on Sep 8, 2022

Commits on Sep 16, 2022

updated svclone container to include bugfix
anoronh4
committed
88214c9
add copy-number file to svclone inputs
anoronh4
committed
55e4f61
add description and labels to prepare_svclone_inputs.py
anoronh4
committed
fde42d5

Commits on Sep 19, 2022

fix input channels for sv_wf
anoronh4
committed
d618365

Commits on Sep 28, 2022

Partial documentation updates.
Adam Price
committed
055e026
Update documentation for DSL2.
Adam Price
committed
fd7129b
Merge pull request #973 from mskcc/dsl2/documentation_updates
price0416
authored
1e285fd

Commits on Oct 15, 2022

add calculation of read length, max copy number and mean coverage for svclone configuration
anoronh4
committed
212cc3f

Commits on Oct 18, 2022

updated docs for enhanced SV workflow (#971)
anoronh4
authored
9ea1c50

Commits on Nov 3, 2022

Commits on Nov 4, 2022

add somatic WES support for SvABA
anoronh4
committed
1ad44a7
Merge branch 'develop' of github.com:mskcc/tempo into dsl2/enhancement/WGS_SV
anoronh4
committed
5c9ff2f

Commits on Nov 11, 2022

bugfix
anoronh4
committed
0b11008
Merge branch 'dsl2/enhancement/svaba_wes' into dsl2/enhancement/WGS_SV
anoronh4
committed
af8b661

Commits on Nov 14, 2022

update brass container to include bcftools 1.9
anoronh4
committed
973f5f0
add filtering of BRASS results to remove invalid records where POS or END == 0
anoronh4
committed
49588d6
edit comment about source of sampleStatistics file
anoronh4
committed
aa057d9
Merge branch 'dsl2/bugfix/removeBrassPos0' into dsl2/enhancement/WGS_SV
anoronh4
committed
4c2536d
Revert "update brass to include bcftools version 1.9"
anoronh4
committed
4c69d95
fix bug in ClusterSV process
anoronh4
committed
846a14d
fix resources for GermlineAnnotateSVBedpe
anoronh4
committed
66f2698
fix cardinality of elements in GermlineAnnotateSVBedpe.out.SVAnnotBedpe4Aggregate channel
anoronh4
committed
24676a2
bugfix
anoronh4
committed
270925f

Commits on Nov 15, 2022

Commits on Nov 18, 2022

Commits on Nov 28, 2022

add biocircos plotting module for somatic SV/CNV calls
anoronh4
committed
2858f76

Commits on Nov 29, 2022

add biocircos plotting module for somatic SV/CNV calls
anoronh4
committed
d10cbf4

Commits on Nov 30, 2022

Commits on Dec 1, 2022

Fix publish of svclone results to outDir
anoronh4
committed
a167d1a

Commits on Dec 2, 2022

Commits on Dec 7, 2022

Commits on Dec 9, 2022

added aggregation process for SVclone
anoronh4
committed
ca126e7

Commits on Dec 12, 2022

remove commented lines for clean-up
anoronh4
committed
c8785a5
update docs
anoronh4
committed
c61128a
Merge branch 'dsl2/enhancement/WGS_SV' into dsl2/enhancement/SV_Sigs
anoronh4
committed
dc4e2cb
fix headers in bedpe
anoronh4
committed
0ba9c61

Commits on Dec 16, 2022

Merge pull request #969 from mskcc/dsl2/enhancement/SV_Sigs
anoronh4
authored
48e2a5b

Commits on Dec 19, 2022

Commits on Dec 22, 2022

Commits on Mar 16, 2023

Merge pull request #979 from mskcc/bugfix/workflow_logic_issues
gongyixiao
authored
7071560
change for somatic snv workflow
gongyixiao
authored
1f39fb9
Update GermlineCombineHaplotypecallerVcf.nf
gongyixiao
authored
4abc6f8

Commits on Mar 31, 2023

Added vcf-validator check for processes that run Strelka
anoronh4
committed
eada9af

Commits on Apr 4, 2023

Merge pull request #983 from mskcc/bugfix/strelka_validation
anoronh4
authored
5066bde

Commits on Apr 20, 2023

define intermediates_dir for rmarkdown rendering
anoronh4
committed
94e6c7b

Commits on May 6, 2023

Merge pull request #985 from mskcc/bugfix/svcircos_intermediates
anoronh4
authored
ffa3a19

Commits on May 23, 2023

Empty-Commit to restart travis
anoronh4
committed
fad173e

Commits on Jun 15, 2023

Commits on Jun 30, 2023

Switched facets annotation to using hisens results rather than purity
anoronh4
committed
272f4e1

Commits on Nov 2, 2023

fix empty headerless bedpe
anoronh4
committed
42346d6
handle empty iannotatesv result
anoronh4
committed
74245e2
removed extra bedpe columns for bedpe with no variants
anoronh4
committed
2f09d6a
fixed output file generation
anoronh4
committed
5af2333

Commits on Nov 3, 2023

Commits on Nov 21, 2023

Merge pull request #996 from mskcc/master
johnoooh
authored
2131bf5

Commits on Dec 21, 2023

Merge pull request #987 from mskcc/bugfix/hisens_zygosity
anoronh4
authored
9205f8f

Commits on Jan 29, 2024

Merge pull request #993 from mskcc/bugfix/headerless_bedpe
anoronh4
authored
b52ffe8

Commits on Jan 30, 2024

enabled storeDir for bam alignmnet
Anne Marie Noronha
committed
6e6dc3f
removed non-input-context values from process outputs for DoFacets
Anne Marie Noronha
committed
8268a75
removed non-input-context values from process outputs for RunLOHHLA and RunPolysolver
Anne Marie Noronha
committed
2ec7701
removed non-input-context values from process outputs for RunNeoantigen
Anne Marie Noronha
committed
e50f08c
removed non-input-context values from process outputs for SomaticFacetsAnnotation
Anne Marie Noronha
committed
e7fa978
removed non-input-context values from process outputs for MetaDataParser
Anne Marie Noronha
committed
50464a5
removed non-input-context values from process outputs for QcConpair and QcConpairAll
Anne Marie Noronha
committed
7a2a672
removed non-input-context values from process outputs for HRDetect
Anne Marie Noronha
committed
1aaeb7a
Merge branch 'develop' into enhancement/storedir_enable
Anne Marie Noronha
committed
2728843
removed non-input-context values from process outputs for SomaticAnnotateSVBedpe and SomaticRunClusterSV
Anne Marie Noronha
committed
045ceb3
removed non-input-context values from process outputs for SomaticRunClusterSV
Anne Marie Noronha
committed
91f9811

Commits on Feb 12, 2024

removed non-input-context values from process outputs for GermlineCombineHaplotypecallerVcf, GermlineFacetsAnnotation, GermlineRunStrelka2
Anne Marie Noronha
committed
d2bcb43
update google drive url for test dataset
Anne Marie Noronha
committed
ebc83c6

Commits on Feb 23, 2024

Empty-Commit
Anne Marie Noronha
committed
76bef36

Commits on Mar 6, 2024

removed deprecated pipeline.nf mentions from docs
Anne Marie Noronha
committed
4ab6272
update test-data link for travis
Anne Marie Noronha
committed
a1ef26e

Commits on Mar 7, 2024

Merge pull request #1006 from mskcc/update/travis_testdata_link
anoronh4
authored
e8f1538
Merge branch 'develop' into update/remove_pipeline_nf_docs
Anne Marie Noronha
committed
7208f91
fix broken links to exome and genome configs
Anne Marie Noronha
committed
d3d8a1f

Commits on Mar 8, 2024

Merge pull request #1005 from mskcc/update/remove_pipeline_nf_docs
anoronh4
authored
f2eca14

Commits on Apr 12, 2024

emit original quals
Anne Marie Noronha
committed
fc7837f
Merge pull request #1008 from mskcc/emit_OQ
anoronh4
authored
e103242

Commits on Apr 24, 2024

Merge pull request #1003 from mskcc/enhancement/storedir_enable
anoronh4
authored
3c38d2e

Commits on Jul 19, 2024

fix conpair channel
tempo bot
committed
9f06d7a
remove unused channel
anoronh4
committed
a0634a4

Commits on Jul 22, 2024

Merge pull request #1013 from mskcc/bugfix/conpair_channel
anoronh4
authored
3d828d1

Commits on Nov 15, 2024

remove header
gongyixiao
committed
633d74a
sym link
gongyixiao
committed
0a98fa3
change links
gongyixiao
committed
8fbc447
fix
gongyixiao
committed
b66239d
fix pngs
gongyixiao
committed
1c52ac7

Commits on Nov 21, 2024

replace taylorlab path to tempo path
gongyixiao
committed
d21fa9a

Commits on Dec 3, 2024

Updated dockerfile, module script
johnoooh
committed
2856843

Commits on Dec 4, 2024

lil url update
johnoooh
committed
a8f3006
version update
johnoooh
committed
da4abe8
Update containers.config
johnoooh
committed
a3d7dd0

Commits on Dec 6, 2024

Commits on Dec 10, 2024

Merge pull request #1020 from mskcc/bugfix/germline_bedpe_header
anoronh4
authored
f8c763a

Commits on Dec 13, 2024

Commits on Jun 9, 2025

Merge pull request #1023 from mskcc/bugfix/taylorlab_path
gongyixiao
authored
4db11c9
Minor documentation updates.

Adam Price
authored and
gongyixiao
committed
2555d04

Commits on Jun 10, 2025

Update config.yml
gongyixiao
authored
b84440d
Merge pull request #1025 from mskcc/dsl2/documentation_updates
gongyixiao
authored
f0c6b12
Merge pull request #1029 from mskcc/bugfix/netlify
gongyixiao
authored
7b160b2
fix node.js version for netlify deploy
gongyixiao
authored
b3a1090
Merge pull request #1030 from mskcc/bugfix/netlify_node_js_version_18
gongyixiao
authored
ab27690
add README.md into docs
gongyixiao
committed
9f88e80

Commits on Jun 11, 2025

Merge pull request #1031 from mskcc/bugfix/netlify
gongyixiao
authored
6988849
update dag
gongyixiao
committed
1ab52f5

Commits on Jun 12, 2025

Merge pull request #1032 from mskcc/enhancement/dag
gongyixiao
authored
e3f79f9

Commits on Jun 24, 2025

neoantigen parallel
gongyixiao
committed
52b16b3

Commits on Jun 26, 2025

Commits on Sep 29, 2025

Commits on Sep 30, 2025

Merge pull request #1038 from mskcc/bug/CollectHsMetrics_coverage_cap_increase
gongyixiao
authored
eafb3a4

Commits on Dec 12, 2025

updated outputs.md
anoronh4
committed
5f32779

Commits on Jan 8, 2026

Merge pull request #1041 from mskcc/enhancement/tempo_2.0.0_documentation
anoronh4
authored
fdf4376

Commits on Jan 16, 2026

Commits on Jan 29, 2026

Fix Travis CI: Mock OncoKB & update test commands (backport from MSK-Staging#1)
Yixiao Gong
committed
367409c
Migrate CI: Add GitHub Actions and remove Travis CI
Yixiao Gong
committed
8063e16
Update CI: Pin Ubuntu 22.04, Java 17 & Nextflow 25.04.7
Yixiao Gong
committed
f72ece0
Update CI: Pin Ubuntu 22.04, Java 17, NXF 25.04.7 & Run on all PRs
Yixiao Gong
committed
89951b5
Fix CI: Explicit PR triggers & enable manual dispatch
Yixiao Gong
committed
ac1db82
Merge remote-tracking branch 'origin/bugfix/nextflow_version' into fix/travis-ci
Yixiao Gong
committed
4f19b07
Merge pull request #1043 from mskcc/fix/travis-ci
gongyixiao
authored
176b5e2
Merge pull request #1042 from mskcc/bugfix/nextflow_version
gongyixiao
authored
f791892

Commits on Feb 5, 2026

Commits on Feb 6, 2026

Merge pull request #1052 from mskcc/bugfix/ci-test
gongyixiao
authored
ef39363