BD2KGenomics toil-scripts issues

BD2KGenomics / toil-scripts

Toil workflows for common genomic pipelines

Apache License 2.0

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issues

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Bump pyyaml from 3.11 to 5.1

#481 dependabot[bot] opened 4 years ago
0
Fix importFile documentation

#480 cket opened 7 years ago
0
Pass job to germline docker call (resolves #478)

#479 jpfeil opened 7 years ago
1
Pass job to germline docker call fuctions

#478 jpfeil opened 7 years ago
0
Insure parse_version does not return tuple (resolves #476)

#477 cket closed 7 years ago
3
Use parse_version

#476 cket closed 7 years ago
0
Update to refactored docker_call (resolves #474)

#475 cket closed 7 years ago
2
Update docker_call invocations

#474 cket closed 7 years ago
0
bwa_alignment broken import on master

#473 jvivian closed 7 years ago
1
update transfer_tcga_to_s3

#472 jvivian closed 7 years ago
0
Fix ADAM/GATK pipeline input errors

#471 jpfeil opened 7 years ago
0
GATK Pipeline Validation Testing

#470 alex-hancock opened 7 years ago
3
Add configurable disk space (resolves #468)

#469 jvivian closed 7 years ago
4
Add configurable disk option to RNA-seq

#468 jvivian closed 7 years ago
1
toil-rnaseq re-run STAR with at least --limitBAMsortRAM fails

#467 Jeltje closed 7 years ago
20
Make sure stdout and stderr from tools are not suppressed in worker log

#466 hannes-ucsc opened 8 years ago
0
Refer to proper version of toil-lib

#465 cket closed 8 years ago
1
Add CKCC QC to Release

#464 jvivian closed 7 years ago
2
Bump toil-lib version to 1.0.4a1.dev55 (resolves #462)

#463 cket closed 8 years ago
2
Bump Toil-lib version to 1.0.4a1.dev55

#462 cket closed 8 years ago
0
Remove CGL RNA-seq pipeline (resolves #446)

#461 jvivian closed 7 years ago
2
rnaseq-cgl non fatal? samtools error

#460 Jeltje closed 7 years ago
6
Stop virtualenv from upgrading setuptools (resolves #458)

#459 cket closed 8 years ago
1
Jenkins builds are not deploying to pypi

#458 cket closed 8 years ago
0
Backport mate-pair heuristic and add disk req (resolves #454, resolves #455)

#457 jvivian closed 8 years ago
5
Readme updates

#456 alex-hancock closed 8 years ago
0
Backport fastq mate pair naming fix to 2.0.x

#455 hannes-ucsc closed 8 years ago
1
Disk requirement missing in rnaseq pipeline

#454 hannes-ucsc closed 8 years ago
1
Cherrypicking disk req to master (resolves #447)

#453 jvivian closed 8 years ago
1
Properly interpolate setup.py help strings (resolves #451)

#452 cket closed 8 years ago
1
Type Error raised when calling setup.py without Toil installed

#451 cket closed 8 years ago
0
README update

#450 alex-hancock closed 8 years ago
0
README now links to dockerized pipeline README

#449 alex-hancock closed 8 years ago
1
Add disk req for STAR (resolves #447)

#448 jvivian closed 8 years ago
2
rnaseq-cgl on aws gets No space left on device errors

#447 Jeltje closed 8 years ago
5
Remove RNA-seq pipeline from toil-scripts

#446 jvivian closed 7 years ago
0
Create job factories that automatically compute requirements

#445 hannes-ucsc closed 7 years ago
3
Request: Accept cram input to toil-exome

#444 Jeltje opened 8 years ago
0
Add dynamic disk allocation (resolves #216)

#443 jvivian closed 8 years ago
4
Create output-dir if it does not exist (resolves #441)

#442 jvivian closed 8 years ago
1
toil-bwa should create output dir if not exists

#441 Jeltje closed 8 years ago
0
Add dynamic disk requirements (resolves #216)

#440 jvivian closed 8 years ago
1
Improve mate pair heuristic (resolves #436)

#439 jvivian closed 8 years ago
8
rnaseq-cgl gets only No log file present errors

#438 Jeltje closed 7 years ago
22
Fix --sample input (resolves #430)

#437 jvivian closed 8 years ago
0
Mate pair designator heuristic fails if parent directory name contains R1 or R2

#436 hannes-ucsc closed 8 years ago
4
Wrap ADAM pipeline calls in logged timers

#435 fnothaft opened 8 years ago
0
Add toil-lib dependency (resolves BD2KGenomics/toil#922)

#434 jvivian closed 8 years ago
8
change STAR outSAMunmapped argument

#433 hbeale opened 8 years ago
0
Error Messages from BWAkit Invocations are not retained in worker.log

#432 alex-hancock closed 8 years ago
1