Ecosyste.ms: Issues

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GitHub / molonc/sisyphus issues and pull requests

#74 - build(deps): bump pyyaml from 3.12 to 5.1 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] about 5 years ago - 1 comment
Labels: dependencies

#73 - Add a function to add/delete datasets from a curation.

Pull Request - State: closed - Opened by sanansakura about 5 years ago

#72 - SISY-176: Compatibility with scpipeline v0.5.0

Pull Request - State: closed - Opened by jeniferpham about 5 years ago

#71 - feature: added S3 storage client

Pull Request - State: closed - Opened by diljotgrewal about 5 years ago

#70 - bugfix: delete file if we intend to overwrite

Pull Request - State: closed - Opened by amcpherson about 5 years ago

#69 - SISY-168: refactor gsc import script

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#68 - SCDNA-209: Select reference genome from taxnomy id

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#67 - SISY-162: refactor pseudobulk inputs.yaml

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#66 - minor: python 3 changes and minor logging fix

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#65 - SISY-164: skip missing files option

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#64 - Sisy 163

Pull Request - State: closed - Opened by mwkyuen over 5 years ago

#63 - CIA-32: tenx workflow

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#62 - CIA-7: added tenx fastq import script

Pull Request - State: closed - Opened by brittanyhewitson over 5 years ago

#60 - SCDNA-177: fixup yaml files with 'boolean'

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#59 - TANTA-164: remove dependency on colossus analysis info

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#57 - Removedeletedfixes

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#56 - refactor search_input_datasets for hmmcopy

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#55 - Scdna 125

Pull Request - State: closed - Opened by svn779 over 5 years ago

#54 - Sisy 150

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#53 - SISY-149: Get or create analysis with right naming convention

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#52 - COLO-93: Find unanalyzed data and create analyses to run

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#51 - Sort sequences by library and instrument before import.

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#50 - fixed SCDNA-124 Create a script to convert hdf5 to csv.gz/yaml

Pull Request - State: closed - Opened by svn779 over 5 years ago

#49 - Sisy 145

Pull Request - State: closed - Opened by amcpherson over 5 years ago

#48 - SISY-116: Generate empty missing fastqs after bcl2fastq

Pull Request - State: closed - Opened by jeniferpham over 5 years ago

#47 - SISY-144: refactored WGS bam import script

Pull Request - State: closed - Opened by brittanyhewitson over 5 years ago

#46 - scripts added

Pull Request - State: closed - Opened by SimongSong over 5 years ago

#45 - added scripts to get ITH filepaths and update patient data

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#44 - final script?

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#43 - Analysis lanes updates

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#42 - Todo 49

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#40 - Pseudobulkautomation

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#39 - TODO-49: make query_gsc_for_wgs_bams run on shahlab15

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#37 - SISY-129: Restructure gsc dlp fastq import

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#36 - Docker

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#34 - SISY-123: Remove file_type

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#33 - Sisy 121

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#32 - SISY117 unanalyzed data script added

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#31 - SISY-119: create / update import cellenone scripts

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#30 - Sisy 113

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#29 - Removed parse arg

Pull Request - State: closed - Opened by SimongSong almost 6 years ago - 1 comment

#28 - Sisy 97

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#27 - SISY-103 refactoring

Pull Request - State: closed - Opened by Mike-Yue almost 6 years ago

#26 - revamped - parsearg replaced with click

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#25 - tanta-110 script added

Pull Request - State: closed - Opened by SimongSong almost 6 years ago

#24 - TANTA-166: Allow for generic analyses

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#23 - added check for tantalus when decompressing spec

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#22 - TANTA 185

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#21 - SISY-90: Pushed fastqs to blob in import scripts

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#20 - Bam import fix

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#19 - Bugfix: Changed file_type to FQ if file is a fastq.

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#18 - Sisy 82

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#17 - TANTA-158: script for adding generic dataset

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#16 - Sisy 78

Pull Request - State: closed - Opened by schan27 almost 6 years ago

#15 - SISY-76: Refactor and fix query_gsc_for_wgs_bams.py

Pull Request - State: closed - Opened by amcpherson almost 6 years ago

#14 - Sisy 76

Pull Request - State: closed - Opened by brittanyhewitson almost 6 years ago

#13 - Sisy 88

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#12 - gzip file check - SISY-86

Pull Request - State: closed - Opened by Mike-Yue almost 6 years ago

#11 - Sisy 87.2

Pull Request - State: closed - Opened by jeniferpham almost 6 years ago

#10 - Testdataset

Pull Request - State: closed - Opened by schan27 almost 6 years ago

#9 - Updateorcreate

Pull Request - State: closed - Opened by amcpherson about 6 years ago

#8 - added file transfer from shahlab to blob

Pull Request - State: closed - Opened by schan27 about 6 years ago

#7 - Scdna 19

Pull Request - State: closed - Opened by amcpherson about 6 years ago

#6 - remove sequence_lanes from inputs yaml

Pull Request - State: closed - Opened by schan27 about 6 years ago

#5 - Sisy 68

Pull Request - State: closed - Opened by Mike-Yue about 6 years ago

#4 - working results import

Pull Request - State: closed - Opened by schan27 about 6 years ago

#3 - bugfix: strip prefix for blob if it exists

Pull Request - State: closed - Opened by schan27 about 6 years ago

#2 - Tanta 87

Pull Request - State: closed - Opened by amcpherson about 6 years ago

#1 - use tantalus client dbclients and minor fixes

Pull Request - State: closed - Opened by schan27 about 6 years ago