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somatic_dna_wdl

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Commits

AuthorCommitMessageCommit dateIssues
Manisha KherManisha Kher
4e0245a342dMMerge branch 'master' into wgs_exome_merge_sweng
Manisha KherManisha Kher
502581e347eTWDL-270: New thresholds for QC checkTWDL-270
Manisha KherManisha Kher
895981fed13Increase time limits for some tasks
Manisha KherManisha Kher
705c1a153d0Set LANG in GatkMergeVcf to handle accented characters correctly.
Manisha KherManisha Kher
fee640b0c9bMinor changes after review
Manisha KherManisha Kher
d7865e6b62bTWDL-298: Remove read_* calls from tasks.TWDL-298
Manisha KherManisha Kher
4bc9fafcd84TWDL-290: Added struct sam which can handle cram or bam. Added missingqos and partition to many workflows.TWDL-290
Manisha KherManisha Kher
0720bdba587MMerge branch 'lancet2' into wgs_exome_merge_sweng
Manisha KherManisha Kher
a83983f7b73Merge branch Lancet2. Add parameters for qos and paritition.commit db56ac70136cda3da035dd1dbf43bfca0623f25b Author: Jennifer Shelton <jshelton@nygenome.org> Date: Thu Oct 30 10:21:39 2025 -0400 feat: add longRun option to alignment tasks which run on the merged BAM commit 15ee2a46a5bfb9896d6a8e952330e805f4e26c83 Author: Manisha Kher <mkher@nygenome.org> Date: Thu Oct 30 06:48:59 2025 -0400 Increased runtime_minutes to a large value. T...TWDL-280
Jennifer SheltonJennifer Shelton
ecb6cde1230fix: pass through normal info
Jennifer SheltonJennifer Shelton
7151f92472bfeat: ichorCNA workflow added
Jennifer SheltonJennifer Shelton
56028cc9abefix: recover is preemption leaves symbolic link for bam.bai suffix
Jennifer SheltonJennifer Shelton
db56ac70136feat: add longRun optino to alignment taskswhich run on the merged BAM
Jennifer SheltonJennifer Shelton
5bb44fb6c53feat: handle unusual deconstructsig runs
Jennifer SheltonJennifer Shelton
ac5bb514221refactor: limit max preemptions
Manisha KherManisha Kher
0780e0d3481Add bwamem2Mem and novosortMem to preprocessing_wkf.wdl
Jennifer SheltonJennifer Shelton
ab1adccd434feat: convert only one cram to bam if neededspeed up gridss runs
Jennifer SheltonJennifer Shelton
e3beb753369refactor: slurm efficiency adjustments
Jennifer SheltonJennifer Shelton
00faa13edd3fix: update thread adjustment for hyperthreads
Jennifer SheltonJennifer Shelton
c1b0e542293fix: draft changes for contemporary normal pairings
Manisha KherManisha Kher
a8439358aacCheck for haplotype input before running baf.
Jennifer SheltonJennifer Shelton
97526eff531feat: minor changes to preemptible slurm runsadditional workflow for no scale BicSeq2 runs
Manisha KherManisha Kher
99e23c97725MPull request #60: Merging lancet2 into wgs_exome_merge_swengMerge in WDL/somatic_dna_wdl from lancet2_testing to wgs_exome_merge_sweng * commit 'd096a329ac62fd2a16a8ca8e10af08e279110022': Pass qos and partition parameters to the post_processing_wkf. Minor reorg of germline outputs. Small changes found in testing. Testing merge from lancet2 branch feat: bump up tie limit for FFPE pairs feat: automatically set the high mem flags for FFPE pair...
Manisha KherManisha Kher
d096a329ac6Pass qos and partition parameters to the post_processing_wkf.
Manisha KherManisha Kher
49380faffd7Minor reorg of germline outputs.
Manisha KherManisha Kher
2dbe1ca9c94Small changes found in testing.
Jennifer SheltonJennifer Shelton
2ced1f1dd2efeat: add custom tasks that will restart- with zero preemptions - with more mem on slurm if the initial run fails with [0, 79, 137, 255] and the bioinformatics tool doesn't have a return code of 0
Jennifer SheltonJennifer Shelton
93c92c2ae09refactor: reduce request
Manisha KherManisha Kher
484de464a46Testing merge from lancet2 branch
Jennifer SheltonJennifer Shelton
f919c9535bffeat: reduce requests to scheduler
Jennifer SheltonJennifer Shelton
da3c19fde55dependencies.zip
Jennifer SheltonJennifer Shelton
a0f4e6fc1abfeat: skip germline if preexists
Jennifer SheltonJennifer Shelton
ccbd4777d9drefactor: increase mem efficency and use memory_retry_multiplier
Jennifer SheltonJennifer Shelton
40d42c11cb9refactor: longer GridssPreprocess timelimit
Jennifer SheltonJennifer Shelton
c6fdf054299Mfeat: remove binest coverage plot
Jennifer SheltonJennifer Shelton
7d4b5f102d2fix: for when grep count of 0 causes a non-zero exit code
Manisha KherManisha Kher
bf9045d5022MPull request #59: TWDL-260: Include novosort dedup log in outputs.Merge in WDL/somatic_dna_wdl from TWDL-260_dedup_log to wgs_exome_merge_sweng * commit 'cb96d799336d52a4e64a066fd0159c5721595af8': TWDL-260: Include novosort dedup log in outputs.TWDL-260
Jennifer SheltonJennifer Shelton
5690fab5237feat: minor adjustments
Manisha KherManisha Kher
cb96d799336TWDL-260: Include novosort dedup log in outputs.TWDL-260
Jennifer SheltonJennifer Shelton
6ba0b372e05fix: use analysis Id for high confidence filename
Jennifer SheltonJennifer Shelton
3f0f67cdc97feat: remove binest coverage plot
Jennifer SheltonJennifer Shelton
b1d0fe0eec5Mupdated zipped file
Jennifer SheltonJennifer Shelton
c2129e9af92updated zipped file
Jennifer SheltonJennifer Shelton
ff8d20db2beMfeat: merge dependencies
Jennifer SheltonJennifer Shelton
1a01c87a937refactor: make alignment merge non-preemtibleby default
Jennifer SheltonJennifer Shelton
beadb8f76cdrefactor: update the name in deconstruct_sigs files to client ID
Manisha KherManisha Kher
0a6b42e9df8MMerge branch 'lancet2' into wgs_exome_merge_sweng
Manisha KherManisha Kher
a50fa7f847eMMerge branch 'lancet2' into wgs_exome_merge_sweng
Jennifer SheltonJennifer Shelton
50bc595c901feat: bump up tie limit for FFPE pairs
Jennifer SheltonJennifer Shelton
669561f9d37feat: automatically set thehigh mem flags for FFPE pairs