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somatic_dna_wdl

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  1. WDL Workflows
  2. somatic_dna_wdl

Commits

AuthorCommitMessageCommit dateIssues
Nicolas FourelNicolas Fourel
8fa4987ea86Transferred resources from nygc-comp-s-82ed-resources to nygc-resources-public
Nicolas FourelNicolas Fourel
04e9c5d499fAdded config file for preprocess-only workflow
Nicolas FourelNicolas Fourel
28382d52a02Removed unnecessary runAnalysis variable in somatic_wkf
Nicolas FourelNicolas Fourel
95fe8a91373Workflow is now completing successfully.
Nicolas FourelNicolas Fourel
2bfc7455b79Separated variant calling steps to a new workflow named somatic_analysis_wkf.wdl
Nicolas FourelNicolas Fourel
031876eff45Preliminary workout to separate PP and analysis outputs, not tested!
Nicolas FourelNicolas Fourel
bebe4018638Fix last issues and improved localization logic
Jennifer SheltonJennifer Shelton
2090b693c55feat: allow for transient timeout in kourami reading from bucket
Jennifer SheltonJennifer Shelton
d698885c73dfeat: updated dependencies
Jennifer SheltonJennifer Shelton
43dd5995027feat: additional cosmic 98 files
Jennifer SheltonJennifer Shelton
e883598125ffeat: update support pipelines based on recent changes
Jennifer SheltonJennifer Shelton
79c254a4e03refactor: lower split count based on compbio tests
Jennifer SheltonJennifer Shelton
a9e4a261ddafeat: raise mem based on sweng tests
Jennifer SheltonJennifer Shelton
c4324aaa6bestyle: update name from temp to split
Jennifer SheltonJennifer Shelton
53695e5fac6refactor: decereased disk size request
Jennifer SheltonJennifer Shelton
b7e2157269dfeat: update public docker image
Jennifer SheltonJennifer Shelton
b6a8990125dMfeat: merge sweng updates to master
Jennifer SheltonJennifer Shelton
041e08ea4adfeat: synced cosmic
Nicolas FourelNicolas Fourel
44edafd9f33Updated paths to resource files, updated gcs_htslib_suite and other minor space/memory updates
Jennifer SheltonJennifer Shelton
a46420aabf2feat: update to public docker image
Jennifer SheltonJennifer Shelton
26a9959ff2afeat: add retries for netwrok failures
Jennifer SheltonJennifer Shelton
de96d88eaderefactor: minor changes to number of splits and when service key is used
Jennifer SheltonJennifer Shelton
d98c4c332fdfeat: slice down bams where possible
Manisha KherManisha Kher
b899f4c9c03MMerge branch 'annotation'
Manisha KherManisha Kher
e61d34e38d7MMerge branch 'master' of ssh://bitbucket.nygenome.org:7999/wdl/somatic_dna_wdl
Jennifer SheltonJennifer Shelton
05b60a924dafeat: update dependencies.zip
Jennifer SheltonJennifer Shelton
e066c9b3c60feat: switch to LOCAL preemptible mantabased on TaskComparison
Jennifer SheltonJennifer Shelton
9439f69f1e4feat: switch to LOCAL preemptible gridssbased on TaskComparison
Jennifer SheltonJennifer Shelton
5d2fb8a73cdfeat: decrease VEP threads and membased on TaskComparison
Jennifer SheltonJennifer Shelton
4abe4924bbafeat: decrease lancet threads to 8 and LancetConfirmmem to 40G and splits to 15 based on TaskComparison
Jennifer SheltonJennifer Shelton
ece72a28fdbfix: flag typo
Jennifer SheltonJennifer Shelton
caded0f23b6feat: add dependencies
Jennifer SheltonJennifer Shelton
793b5ac85affeat : minor changes to paths and reports
Jennifer SheltonJennifer Shelton
53707bd0b79fix: minor changes
Jennifer SheltonJennifer Shelton
358fe9de118feat: evenly split lancet intervals
Jennifer SheltonJennifer Shelton
ca54bef64a8stop running gridssAssemble on preemptible machines because preemtions dominate run cost
Jennifer SheltonJennifer Shelton
bbc600dd144feat: switch to HDD for small support file runs
Jennifer SheltonJennifer Shelton
6cfe6cc8380feat: switch to glob to avoid 60s timeout error on prem
Jennifer SheltonJennifer Shelton
028b78c1eddfeat: filter for 1000G and Gnomad after renaming 1000G annotation
Manisha KherManisha Kher
8de488aedf4Increase disksize for some gridss tasks.
Jennifer SheltonJennifer Shelton
025504ebe92fix: changes to somatic pipeline
Jennifer SheltonManisha KherJennifer Shelton
8b089dbabe7MPull request #46: AnnotationMerge in WDL/somatic_dna_wdl from annotation to master * commit '1cb771ac9786e43fd1dc06eb1d2396c7e7e105b4': (22 commits) feat: switch to version with germ_filter_vcf.py added feat: handle runs with no pre-existing split vcfs feat: split mnvs into unique file if applicable remove potential glob matches as hedge against input name matching glob fail at first failing step test: fail at th...
Manisha KherManisha Kher
ee60e6552c6MPull request #45: TWDL-30: Pass novosort licence file as a parameter.Merge in WDL/somatic_dna_wdl from TWDL-30_novosort_license to master * commit '9f373d57d0d9f09281fd5a7e0bab40ac11d50610': Reset lancet threads back to 8. Correct value returned for SomaticQcPass. TWDL-30: Pass novosort licence file as a parameter. Bug fixesTWDL-30
Jennifer SheltonJennifer Shelton
1cb771ac978feat: switch to version with germ_filter_vcf.py added
Jennifer SheltonJennifer Shelton
a3b659a404ffeat: handle runs with no pre-existing split vcfs
Jennifer SheltonJennifer Shelton
c339ebaa566feat: split mnvs into unique fileif applicable remove potential glob matches as hedge against input name matching glob fail at first failing step
Jennifer SheltonJennifer Shelton
3d244fbc7batest: fail at the first command to fail
Manisha KherManisha Kher
9f373d57d0dReset lancet threads back to 8.
Jennifer SheltonJennifer Shelton
962ef024d29feat: use gcs_htslib_suite with germ_filter_vcf.py
Jennifer SheltonJennifer Shelton
7865a5bde23Mpull new docker imageMerge branch 'annotation' of https://bitbucket.nygenome.org/scm/wdl/somatic_dna_wdl into annotation