Nicolas Fourel (Consultant) 8fa4987ea86 Copy commit hash Transferred resources from nygc-comp-s-82ed-resources to nygc-resources-public 03 Sep 2024 Nicolas Fourel (Consultant) 04e9c5d499f Copy commit hash Added config file for preprocess-only workflow 08 Jan 2024 Nicolas Fourel (Consultant) 28382d52a02 Copy commit hash Removed unnecessary runAnalysis variable in somatic_wkf 08 Jan 2024 Nicolas Fourel (Consultant) 95fe8a91373 Copy commit hash Workflow is now completing successfully. 19 Dec 2023 Nicolas Fourel (Consultant) 2bfc7455b79 Copy commit hash Separated variant calling steps to a new workflow named somatic_analysis_wkf.wdl 08 Dec 2023 Nicolas Fourel (Consultant) 031876eff45 Copy commit hash Preliminary workout to separate PP and analysis outputs, not tested! 05 Dec 2023 Nicolas Fourel (Consultant) bebe4018638 Copy commit hash Fix last issues and improved localization logic 07 Nov 2023 Jennifer Shelton 2090b693c55 Copy commit hash feat: allow for transient timeout in kourami reading from bucket 13 Oct 2023 Jennifer Shelton d698885c73d Copy commit hash feat: updated dependencies 12 Oct 2023 Jennifer Shelton 43dd5995027 Copy commit hash feat: additional cosmic 98 files 12 Oct 2023 Jennifer Shelton e883598125f Copy commit hash feat: update support pipelines based on recent changes 11 Oct 2023 Jennifer Shelton 79c254a4e03 Copy commit hash refactor: lower split count based on compbio tests 11 Oct 2023 Jennifer Shelton a9e4a261dda Copy commit hash feat: raise mem based on sweng tests 11 Oct 2023 Jennifer Shelton c4324aaa6be Copy commit hash style: update name from temp to split 05 Oct 2023 Jennifer Shelton 53695e5fac6 Copy commit hash refactor: decereased disk size request 05 Oct 2023 Jennifer Shelton b7e2157269d Copy commit hash feat: update public docker image 03 Oct 2023 Jennifer Shelton b6a8990125d M Copy commit hash feat: merge sweng updates to master 03 Oct 2023 Jennifer Shelton 041e08ea4ad Copy commit hash feat: synced cosmic 03 Oct 2023 Nicolas Fourel (Consultant) 44edafd9f33 Copy commit hash Updated paths to resource files, updated gcs_htslib_suite and other minor space/memory updates 29 Sep 2023 Jennifer Shelton a46420aabf2 Copy commit hash feat: update to public docker image 29 Sep 2023 Jennifer Shelton 26a9959ff2a Copy commit hash feat: add retries for netwrok failures 28 Sep 2023 Jennifer Shelton de96d88eade Copy commit hash refactor: minor changes to number of splits and when service key is used 25 Sep 2023 Jennifer Shelton d98c4c332fd Copy commit hash feat: slice down bams where possible 08 Sep 2023 Manisha Kher b899f4c9c03 M Copy commit hash Merge branch 'annotation' 05 Sep 2023 Manisha Kher e61d34e38d7 M Copy commit hash Merge branch 'master' of ssh://bitbucket.nygenome.org:7999/wdl/somatic_dna_wdl 05 Sep 2023 Jennifer Shelton 05b60a924da Copy commit hash feat: update dependencies.zip 31 Aug 2023 Jennifer Shelton e066c9b3c60 Copy commit hash feat: switch to LOCAL preemptible manta based on TaskComparison 31 Aug 2023 Jennifer Shelton 9439f69f1e4 Copy commit hash feat: switch to LOCAL preemptible gridss based on TaskComparison 31 Aug 2023 Jennifer Shelton 5d2fb8a73cd Copy commit hash feat: decrease VEP threads and mem based on TaskComparison 31 Aug 2023 Jennifer Shelton 4abe4924bba Copy commit hash feat: decrease lancet threads to 8 and LancetConfirm mem to 40G and splits to 15 based on TaskComparison 31 Aug 2023 Jennifer Shelton ece72a28fdb Copy commit hash fix: flag typo 23 Aug 2023 Jennifer Shelton caded0f23b6 Copy commit hash feat: add dependencies 21 Aug 2023 Jennifer Shelton 793b5ac85af Copy commit hash feat : minor changes to paths and reports 20 Aug 2023 Jennifer Shelton 53707bd0b79 Copy commit hash fix: minor changes 20 Aug 2023 Jennifer Shelton 358fe9de118 Copy commit hash feat: evenly split lancet intervals 20 Aug 2023 Jennifer Shelton ca54bef64a8 Copy commit hash stop running gridssAssemble on preemptible machines because preemtions dominate run cost 18 Aug 2023 Jennifer Shelton bbc600dd144 Copy commit hash feat: switch to HDD for small support file runs 18 Aug 2023 Jennifer Shelton 6cfe6cc8380 Copy commit hash feat: switch to glob to avoid 60s timeout error on prem 18 Aug 2023 Jennifer Shelton 028b78c1edd Copy commit hash feat: filter for 1000G and Gnomad after renaming 1000G annotation 17 Aug 2023 Manisha Kher 8de488aedf4 Copy commit hash Increase disksize for some gridss tasks. 15 Aug 2023 Jennifer Shelton 025504ebe92 Copy commit hash fix: changes to somatic pipeline 10 Aug 2023 Jennifer Shelton 8b089dbabe7 M Copy commit hash Pull request #46: Annotation Merge 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... 29 Jul 2023 Manisha Kher ee60e6552c6 M Copy commit hash Pull 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 fixes 24 Jul 2023 TWDL-30 Jennifer Shelton 1cb771ac978 Copy commit hash feat: switch to version with germ_filter_vcf.py added 17 Jul 2023 Jennifer Shelton a3b659a404f Copy commit hash feat: handle runs with no pre-existing split vcfs 16 Jul 2023 Jennifer Shelton c339ebaa566 Copy commit hash feat: split mnvs into unique file if applicable
remove potential glob matches as hedge against input name
matching glob
fail at first failing step 16 Jul 2023 Jennifer Shelton 3d244fbc7ba Copy commit hash test: fail at the first command to fail 14 Jul 2023 Manisha Kher 9f373d57d0d Copy commit hash Reset lancet threads back to 8. 12 Jul 2023 Jennifer Shelton 962ef024d29 Copy commit hash feat: use gcs_htslib_suite with germ_filter_vcf.py 11 Jul 2023 Jennifer Shelton 7865a5bde23 M Copy commit hash pull new docker image Merge branch 'annotation' of https://bitbucket.nygenome.org/scm/wdl/somatic_dna_wdl into annotation 11 Jul 2023 
Nicolas Fourel (Consultant)