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2.0 #1021

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gongyixiao and others added 30 commits March 10, 2022 15:35
@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
allow for empty hsmetrics input in SampleRunMultiQC
de1007d
@anoronh4
remove vcf entries without "END=" attribute for downstream processing
e27b46d
@anoronh4
map svclass values to acceptable values for HRDetect
59b4bf9
@anoronh4
allow for empty hsmetrics input in CohortRunMultiQC and QcBamAggregate
2bc7af8
@gongyixiao
Merge pull request #958 from mskcc/bugfix/HsMetricsInput4WGS
9610e84 
Bugfix - HsMetrics Input for WGS
@anoronh4
generate outputs in facets that are compatible with BRASS and HRDetec…
c225338 
…t (similar to ascat)
@gongyixiao
Update GermlineFacetsAnnotation.nf
a3ba1bf
@gongyixiao
fix tag warning
50f6fe9
@gongyixiao
associate errorStrategy with maxRetries
8ed7353
@anoronh4
reorganize Bedpe annotation and filtering steps, and renamed certain …
ae857d0 
…processes
@anoronh4
update to reflect changes in filtering processes and renaming of thos…
4fbd110 
…e processes
@anoronh4
remove brassRefDir and vagrentRefDir from referenceMap result when th…
30ae803 
…e workflow profile is 'test'
@anoronh4
updated bedpe handling scripts and moved them to folder for iannotate…
5debf04 
…sv, to reflect that they are executed in the same containers as the iannotatesv tool
@anoronh4
add script that generates outputs in facets that are compatible with …
8059875 
…BRASS and HRDetect
@anoronh4
updated filtering of vcf so that variants with insufficient number of…
9de96d5 
… callers are filtered, and variants that are not properly formatted are discarded.
@anoronh4
updated svtools docker to remove annotsv
d7e5e17
Anne Marie Noronha and others added 29 commits February 12, 2024 13:36
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
fix conpair channel
8677054
@anoronh4
remove unused channel
d3a3f99
@anoronh4
Merge pull request #1013 from mskcc/bugfix/conpair_channel
e3efea9 
fix conpair channel
@gongyixiao
remove header
c9c76ca
@gongyixiao
sym link
e5c7731
@gongyixiao
change links
ebc7afd
@gongyixiao
fix
3c86afb
@gongyixiao
fix pngs
3a82186
@johnoooh
Updated dockerfile, module script
3ea5baf 
Replacing old URL. Couldnt rebuild dockerfile due to R package issues so we chose to build from the old one
@johnoooh
lil url update
a5c3fd3
@johnoooh
version update
4903b57
@johnoooh
Update containers.config
171c84d
@anoronh4
fix missing header for empty germline bedpe files
b586b24
@anoronh4
disable SomaticRunSVCircos process when running with the smallGRCh37 …
c3a3594 
…genome
@anoronh4
Merge pull request #1020 from mskcc/bugfix/germline_bedpe_header
a1a17c9 
fix failing SV processes in travis CI tests
@gongyixiao
Merge pull request #1019 from mskcc/bugfix/oncokb_link
58ad1f7 
Update oncokb link
@gongyixiao
Merge pull request #1016 from mskcc/enhancement/docs
8e4d68f 
Enhancement/docs
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4 participants
@gongyixiao @anoronh4 @price0416 @johnoooh