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Feature/upgrade delly v126 #1012

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Feature/upgrade delly v126 #1012

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Addresses 1011

gongyixiao and others added 30 commits February 24, 2022 14:58
@gongyixiao
Merge pull request #949 from mskcc/dsl2/full_travis_test
8891431 
Dsl2/full travis test
@anoronh4
bugfix
0ddca1c
@gongyixiao
change scatterCount to 3 for travis test
3fac146
@anoronh4
add brass references
1dd457f
@anoronh4
add resources for BRASS-related processes
a850133
@anoronh4
add brass references to defineReferenceMap method
6c2fbc1
@anoronh4
bugfixes in BRASS workflow
4897048
@anoronh4
bugfix ascat
8a0fb7d
@anoronh4
add output for Facets to try with HrDetect and add toggle to switch b…
eb3f57f 
…etween Facets and Ascat
@anoronh4
bugfix so that bed files are used for all samples that are exome in Q…
6fee282 
…cAlfred
@gongyixiao
fix bam size calculation issue
d5bb63e
@gongyixiao
fixing the same thign in pipeline.nf
7b3c1da
@gongyixiao
forgot something
88f15a8
@gongyixiao
Update pipeline.nf
bfa8e21
@gongyixiao
Merge pull request #954 from mskcc/dsl2/bugfix/alfred_target
0ee1177 
QcAlfred target bugfix
@gongyixiao
Merge pull request #955 from mskcc/dsl2/bugfix/MergeBamsAndMarkDuplic…
1fffc46 
…ates

fix bam size calculation issue
@gongyixiao
Merge pull request #951 from mskcc/dsl2/master
32d0a82 
Dsl2/master
@anoronh4
update test-data references and bugfixes
0f7723c
@anoronh4
exclude .pyc files from git versioning
f375f10
@anoronh4
formalized input of SV calls to the SomaticMergeDellyandManta process…
4cd4204 
…, and reorganized brass processes
@anoronh4
remove deprecated BRASS file
e6ee0e3
@anoronh4
updated SvABA resource allocation
c0331fe
@anoronh4
reverted original file to make it distinct from sv_wf_new.nf
b8b33c9
@anoronh4
merge in fixed conflicts
b1ceb0b
@anoronh4
changed name SomaticMergeDellyAndManta in configs to to SomaticMergeSVs
7971358
@anoronh4
changed old process SomaticMergeDellyAndManta to replace names relate…
db51f06 
…d to delly+manta to merging
@anoronh4
edited paths of included module files
aa69904
@anoronh4
split tuple of references into individual inputs
3eef300
@anoronh4
created outputs of Facets that can be used as inputs in BRASS, coloca…
739603b 
…ting it with the output generation for HRDetect in a custom R script
@anoronh4
bugfix for hsMetrics channel for when assayType == 'genome'
7fe6da8
anoronh4 and others added 29 commits November 3, 2023 13:52
@anoronh4
Merge pull request #991 from mskcc/master
691e767 
Merge hotfix/1.4.4 back into develop
@anoronh4
Merge pull request #981 from mskcc/bugfix/shorten_combine_mutect2_vcf…
eda44bc 
…_cmd

Bugfix/shorten combine mutect2 vcf cmd
@johnoooh
Merge pull request #996 from mskcc/master
e98d057 
Merge master hotfix back into develop
@anoronh4
Merge pull request #987 from mskcc/bugfix/hisens_zygosity
e29f5be 
Fixed facets zygosity annotation of maf
@anoronh4
Merge pull request #993 from mskcc/bugfix/headerless_bedpe
2ae9e66 
fix empty bedpe
enabled storeDir for bam alignmnet
9b69e11
removed non-input-context values from process outputs for DoFacets
d53e18d
removed non-input-context values from process outputs for RunLOHHLA a…
a24422e 
…nd RunPolysolver
removed non-input-context values from process outputs for RunNeoantigen
a403a4b
removed non-input-context values from process outputs for SomaticFace…
f7896ae 
…tsAnnotation
removed non-input-context values from process outputs for MetaDataParser
d804f88
removed non-input-context values from process outputs for QcConpair a…
f5c7e6b 
…nd QcConpairAll
removed non-input-context values from process outputs for HRDetect
cf3fc86
Merge branch 'develop' into enhancement/storedir_enable
5695611
removed non-input-context values from process outputs for SomaticAnno…
81ab9d8 
…tateSVBedpe and SomaticRunClusterSV
removed non-input-context values from process outputs for SomaticRunC…
997b1fa 
…lusterSV
removed non-input-context values from process outputs for GermlineCom…
1a9fe95 
…bineHaplotypecallerVcf, GermlineFacetsAnnotation, GermlineRunStrelka2
update google drive url for test dataset
4e7e374
Empty-Commit
4d0cbfc
removed deprecated pipeline.nf mentions from docs
5f557d1
update test-data link for travis
528e54e
@anoronh4
Merge pull request #1006 from mskcc/update/travis_testdata_link
9207d0c
Merge branch 'develop' into update/remove_pipeline_nf_docs
1ecff22
fix broken links to exome and genome configs
5753bb0
@anoronh4
Merge pull request #1005 from mskcc/update/remove_pipeline_nf_docs
4400235 
removed deprecated pipeline.nf mentions from docs
emit original quals
c16a7fa
@anoronh4
Merge pull request #1008 from mskcc/emit_OQ
87cada3 
emit original quals
@anoronh4
Merge pull request #1003 from mskcc/enhancement/storedir_enable
9b2da47 
enabled storeDir for dsl2
updated delly and htslib in delly-bcftools docker image
8bcbf29
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4 participants
@anoronh4 @gongyixiao @price0416 @johnoooh