BD2KGenomics/toil-scripts issues and pull requests

#481 - Bump pyyaml from 3.11 to 5.1

Pull Request - State: open - Opened by dependabot[bot] about 5 years ago
Labels: dependencies

#480 - Fix importFile documentation

Issue - State: open - Opened by cket over 7 years ago

#479 - Pass job to germline docker call (resolves #478)

Pull Request - State: open - Opened by jpfeil almost 8 years ago - 1 comment
Labels: ready, in progress

#478 - Pass job to germline docker call fuctions

Issue - State: open - Opened by jpfeil almost 8 years ago
Labels: in progress

#477 - Insure parse_version does not return tuple (resolves #476)

Pull Request - State: closed - Opened by cket almost 8 years ago - 3 comments

#476 - Use parse_version

Issue - State: closed - Opened by cket almost 8 years ago

#475 - Update to refactored docker_call (resolves #474)

Pull Request - State: closed - Opened by cket almost 8 years ago - 2 comments

#474 - Update docker_call invocations

Issue - State: closed - Opened by cket almost 8 years ago

#473 - bwa_alignment broken import on master

Issue - State: closed - Opened by jvivian almost 8 years ago - 1 comment

#472 - update transfer_tcga_to_s3

Issue - State: closed - Opened by jvivian almost 8 years ago

#471 - Fix ADAM/GATK pipeline input errors

Issue - State: open - Opened by jpfeil almost 8 years ago

#470 - GATK Pipeline Validation Testing

Issue - State: open - Opened by alex-hancock almost 8 years ago - 3 comments

#469 - Add configurable disk space (resolves #468)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 4 comments

#468 - Add configurable disk option to RNA-seq

Issue - State: closed - Opened by jvivian about 8 years ago - 1 comment

#467 - toil-rnaseq re-run STAR with at least --limitBAMsortRAM fails

Issue - State: closed - Opened by Jeltje about 8 years ago - 20 comments

#466 - Make sure stdout and stderr from tools are not suppressed in worker log

Issue - State: open - Opened by hannes-ucsc about 8 years ago

#465 - Refer to proper version of toil-lib

Pull Request - State: closed - Opened by cket about 8 years ago - 1 comment

#464 - Add CKCC QC to Release

Issue - State: closed - Opened by jvivian about 8 years ago - 2 comments

#463 - Bump toil-lib version to 1.0.4a1.dev55 (resolves #462)

Pull Request - State: closed - Opened by cket about 8 years ago - 2 comments

#462 - Bump Toil-lib version to 1.0.4a1.dev55

Issue - State: closed - Opened by cket about 8 years ago

#461 - Remove CGL RNA-seq pipeline (resolves #446)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 2 comments
Labels: needs work

#460 - rnaseq-cgl non fatal? samtools error

Issue - State: closed - Opened by Jeltje about 8 years ago - 6 comments
Labels: need info

#459 - Stop virtualenv from upgrading setuptools (resolves #458)

Pull Request - State: closed - Opened by cket about 8 years ago - 1 comment

#458 - Jenkins builds are not deploying to pypi

Issue - State: closed - Opened by cket about 8 years ago
Labels: bug, build

#457 - Backport mate-pair heuristic and add disk req (resolves #454, resolves #455)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 5 comments
Labels: needs work

#456 - Readme updates

Pull Request - State: closed - Opened by alex-hancock about 8 years ago

#455 - Backport fastq mate pair naming fix to 2.0.x

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 1 comment
Labels: bug

#454 - Disk requirement missing in rnaseq pipeline

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 1 comment
Labels: bug, URGENT

#453 - Cherrypicking disk req to master (resolves #447)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 1 comment

#452 - Properly interpolate setup.py help strings (resolves #451)

Pull Request - State: closed - Opened by cket about 8 years ago - 1 comment

#451 - Type Error raised when calling setup.py without Toil installed

Issue - State: closed - Opened by cket about 8 years ago
Labels: bug

#450 - README update

Pull Request - State: closed - Opened by alex-hancock about 8 years ago

#449 - README now links to dockerized pipeline README

Pull Request - State: closed - Opened by alex-hancock about 8 years ago - 1 comment
Labels: URGENT

#448 - Add disk req for STAR (resolves #447)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 2 comments

#447 - rnaseq-cgl on aws gets No space left on device errors

Issue - State: closed - Opened by Jeltje about 8 years ago - 5 comments

#446 - Remove RNA-seq pipeline from toil-scripts

Issue - State: closed - Opened by jvivian about 8 years ago

#445 - Create job factories that automatically compute requirements

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 3 comments

#444 - Request: Accept cram input to toil-exome

Issue - State: open - Opened by Jeltje about 8 years ago
Labels: enhancement

#443 - Add dynamic disk allocation (resolves #216)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 4 comments

#442 - Create output-dir if it does not exist (resolves #441)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 1 comment

#441 - toil-bwa should create output dir if not exists

Issue - State: closed - Opened by Jeltje about 8 years ago

#440 - Add dynamic disk requirements (resolves #216)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 1 comment

#439 - Improve mate pair heuristic (resolves #436)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 8 comments
Labels: needs work

#438 - rnaseq-cgl gets only No log file present errors

Issue - State: closed - Opened by Jeltje about 8 years ago - 22 comments
Labels: need info

#437 - Fix --sample input (resolves #430)

Pull Request - State: closed - Opened by jvivian about 8 years ago

#436 - Mate pair designator heuristic fails if parent directory name contains R1 or R2

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 4 comments

#435 - Wrap ADAM pipeline calls in logged timers

Issue - State: open - Opened by fnothaft about 8 years ago
Labels: spark/adam

#434 - Add toil-lib dependency (resolves BD2KGenomics/toil#922)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 8 comments

#433 - change STAR outSAMunmapped argument

Issue - State: open - Opened by hbeale about 8 years ago

#432 - Error Messages from BWAkit Invocations are not retained in worker.log

Issue - State: closed - Opened by alex-hancock about 8 years ago - 1 comment

#431 - Fix --sample input (resolves #430)

Pull Request - State: closed - Opened by jvivian about 8 years ago

#430 - Fix --sample in bwa pipeline

Issue - State: closed - Opened by jvivian about 8 years ago

#429 - S3 tests should be skipped if bucket can't be accessed

Issue - State: open - Opened by fnothaft about 8 years ago
Labels: bug

#428 - Add ftp as input option (resolves #422)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 1 comment

#427 - Eliminate config options for approximate input file size

Issue - State: open - Opened by hannes-ucsc about 8 years ago
Labels: enhancement

#426 - Support germline joint genotyping and hard filtering

Issue - State: open - Opened by jpfeil about 8 years ago

#425 - Refactor germline shared files download

Issue - State: open - Opened by jpfeil about 8 years ago

#424 - Factor Docker version strings out

Issue - State: open - Opened by fnothaft about 8 years ago

#423 - Add JEXL expressions to germline config

Issue - State: open - Opened by jpfeil about 8 years ago

#422 - Add ftp as URL option

Issue - State: closed - Opened by jvivian about 8 years ago

#421 - Remove redundant passing of cores (resolves #374)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 1 comment

#420 - Add comprehensive tool descriptions (resolves #417, resolves #416)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 6 comments

#419 - toil-rnaseq does not recognize s3 bucket without subdirectory

Issue - State: closed - Opened by Jeltje about 8 years ago - 6 comments
Labels: need info

#418 - Finish production germline pipeline (resolves #401)

Pull Request - State: closed - Opened by jpfeil about 8 years ago - 5 comments

#417 - Add descriptions of tools to documentation

Issue - State: closed - Opened by jvivian about 8 years ago

#416 - Inaccurate readme for exome variant pipeline

Issue - State: closed - Opened by nsjake about 8 years ago - 2 comments

#415 - Fix single-end submission (resolves #413)

Pull Request - State: closed - Opened by jvivian about 8 years ago - 2 comments

#401 - Add clinical variant annotation to germline

Issue - State: closed - Opened by jpfeil about 8 years ago - 2 comments

#387 - Accommodating pipes in programs.py

Pull Request - State: open - Opened by cmarkello about 8 years ago - 23 comments
Labels: ready, needs work

#380 - Add cloud pilot quality control workflows

Issue - State: open - Opened by fnothaft about 8 years ago
Labels: ready, spark/adam, firecloud

#374 - Remove redundant passing of "cores"

Issue - State: closed - Opened by jvivian about 8 years ago

#371 - Support running ADAM natively in adam-pipeline

Issue - State: closed - Opened by fnothaft about 8 years ago
Labels: spark/adam, firecloud

#365 - Add somaticSniper to exome

Issue - State: closed - Opened by jvivian about 8 years ago - 1 comment

#356 - Concurrently running builds may overwrite each other's test outputs

Issue - State: closed - Opened by hannes-ucsc about 8 years ago - 1 comment
Labels: enhancement

#351 - Run adam-pipeline in single machine mode (resolves #210, #329, #371, #325, #326)

Pull Request - State: closed - Opened by fnothaft about 8 years ago - 9 comments
Labels: spark/adam, firecloud

#347 - Exome - Refactor mean insert size

Issue - State: closed - Opened by jvivian about 8 years ago - 4 comments

#339 - Add developer section to root README

Issue - State: closed - Opened by jvivian over 8 years ago - 2 comments

#335 - Refactor gatk germline (resolves #280)

Pull Request - State: closed - Opened by jpfeil over 8 years ago - 32 comments

#330 - Remove duplicated functions in gatk_processing

Issue - State: open - Opened by jvivian over 8 years ago - 1 comment
Labels: planned

#329 - ADAM pipeline inexplicably runs twice

Issue - State: closed - Opened by almussel over 8 years ago
Labels: bug, spark/adam

#326 - Memory settings tuning for ADAM pipeline

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: bug, spark/adam

#325 - Remove spark cluster support

Issue - State: closed - Opened by fnothaft over 8 years ago
Labels: enhancement, spark/adam

#317 - Add bamstats to RNASeq and Exome and alignment pipelines

Issue - State: closed - Opened by briandoconnor over 8 years ago - 1 comment

#309 - Attach Apache 2 license header to all source files

Issue - State: open - Opened by fnothaft over 8 years ago
Labels: ready

#305 - Discuss: Naming convention for pipeline outputs

Issue - State: closed - Opened by jvivian over 8 years ago - 1 comment

#280 - Refactor germline pipeline using common lib

Issue - State: closed - Opened by jpfeil over 8 years ago

#277 - Make stand alone pre-processing pipeline

Issue - State: closed - Opened by jvivian over 8 years ago - 1 comment

#272 - Register RNASeq-CGL to Dockstore

Issue - State: open - Opened by briandoconnor over 8 years ago - 1 comment
Labels: planned

#271 - Refactor MuTect to run by chromosome

Issue - State: closed - Opened by jvivian over 8 years ago - 3 comments
Labels: enhancement

#266 - Add ICGC Storage System support

Issue - State: closed - Opened by briandoconnor over 8 years ago - 2 comments
Labels: enhancement

#252 - Improve user interface for RNAseq container

Issue - State: closed - Opened by jvivian over 8 years ago
Labels: enhancement

#244 - Setup CI for SplAdder pipeline

Issue - State: closed - Opened by jvivian over 8 years ago - 2 comments
Labels: enhancement

#216 - Add dynamic disk resource allocation for rnaseq_cgl

Issue - State: closed - Opened by jvivian over 8 years ago - 4 comments
Labels: enhancement

#210 - Support running ADAM/GATK pipeline on local storage

Issue - State: closed - Opened by fnothaft over 8 years ago - 2 comments
Labels: enhancement, spark/adam, need info

#186 - multiprocessing called from toil leader in gatk_{germline,processing}

Issue - State: open - Opened by fnothaft over 8 years ago - 5 comments
Labels: bug, planned

#80 - Wig output from STAR for the GTEx runs

Issue - State: closed - Opened by melissacline over 8 years ago - 7 comments

#55 - Run real-world pipeline with cwltoil on a multi-node Mesos cluster

Issue - State: open - Opened by jvivian almost 9 years ago - 7 comments
Labels: enhancement, discuss

#54 - Run variant pipeline with hg38 test inputs

Issue - State: closed - Opened by jvivian almost 9 years ago - 7 comments
Labels: task

#46 - Produce inputs for new RNA-Seq pipeline

Issue - State: closed - Opened by jvivian almost 9 years ago - 4 comments

#36 - Add a container for the MuSe variant caller

Issue - State: open - Opened by melissacline almost 9 years ago - 6 comments
Labels: enhancement, ready

GitHub / BD2KGenomics/toil-scripts issues and pull requests