4dn-dcic/dcicwrangling issues and pull requests

#113 - New property or item status change script

Pull Request - State: closed - Opened by aschroed 8 months ago

#112 - new wrangler notebook

Pull Request - State: open - Opened by RahiNav 9 months ago

#111 - Bug fix for pre-release == released to lab for UserContent

Pull Request - State: closed - Opened by aschroed 9 months ago

#110 - update setting to support repliseq v16.1

Pull Request - State: closed - Opened by aschroed about 1 year ago

#109 - Updates to use python versions 3.8 - 3.11

Pull Request - State: closed - Opened by aschroed about 1 year ago

#108 - Fix geo submission script

Pull Request - State: closed - Opened by RahiNav about 1 year ago - 1 comment

#107 - Add opf2eset nb

Pull Request - State: closed - Opened by aschroed about 1 year ago

#106 - Ajs upd get schema fxns

Pull Request - State: closed - Opened by aschroed over 1 year ago

#105 - Update dcic utils used

Pull Request - State: closed - Opened by aschroed over 1 year ago

#104 - Fixed GA publish

Pull Request - State: closed - Opened by dmichaels-harvard over 1 year ago

#103 - Upd chipseq pipe v2.1.6

Pull Request - State: closed - Opened by aschroed over 1 year ago

#102 - updated ubuntu version for running github workflows

Pull Request - State: closed - Opened by aschroed almost 2 years ago

#101 - Upd dcicutils v

Pull Request - State: closed - Opened by aschroed almost 2 years ago

#100 - Add dbxref nb

Pull Request - State: closed - Opened by aschroed almost 2 years ago

#99 - Bump gitpython from 3.1.27 to 3.1.30

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#98 - Bug fix in notebook 04: expsets were not unique in publication

Pull Request - State: closed - Opened by andreacosolo almost 2 years ago

#97 - Channels fix in notebook 04 microscopy

Pull Request - State: closed - Opened by andreacosolo almost 2 years ago - 1 comment

#96 - Bump certifi from 2022.9.14 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#95 - Bump jupyter-core from 4.11.1 to 4.11.2

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#94 - Update notebook 13

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#93 - released to lab is level 8

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#92 - Add notebook to delete uploaded files and linked items

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#91 - DRAFT - Updated the transfer metadata notebook

Pull Request - State: open - Opened by aschroed about 2 years ago

#90 - Geo2fdn update

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#89 - Upd deps

Pull Request - State: closed - Opened by aschroed about 2 years ago - 4 comments

#88 - remove deleted items from store

Pull Request - State: closed - Opened by andreacosolo about 2 years ago - 1 comment

#87 - Bump jupyter-server from 1.16.0 to 1.17.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies

#86 - Add changelog and add test for updating it

Pull Request - State: closed - Opened by aschroed about 2 years ago

#85 - Update scripts

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#84 - check fastqc only for fastq files

Pull Request - State: closed - Opened by andreacosolo about 2 years ago

#83 - handle extra files independently from parent file

Pull Request - State: closed - Opened by andreacosolo over 2 years ago

#82 - Bump nbconvert from 6.5.0 to 6.5.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#81 - Bump mistune from 0.8.4 to 2.0.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#80 - Bump notebook from 6.4.11 to 6.4.12

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#79 - Bump waitress from 2.1.1 to 2.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#78 - add function to duplicate imaging path columns

Pull Request - State: closed - Opened by andreacosolo over 2 years ago

#77 - update notebook functions to use openpyxl

Pull Request - State: closed - Opened by andreacosolo over 2 years ago

#76 - Bump notebook from 6.4.7 to 6.4.10

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#75 - Updated info for pipelines that were not previously added

Pull Request - State: closed - Opened by aschroed over 2 years ago - 1 comment

#74 - Bump jupyter-server from 1.13.3 to 1.15.4

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#73 - Bump waitress from 2.0.0 to 2.1.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#72 - add reference_files as raw files

Pull Request - State: closed - Opened by andreacosolo almost 3 years ago

#71 - resolve duplication issue with cell culture protocols

Pull Request - State: closed - Opened by andreacosolo almost 3 years ago

#70 - Update dependencies

Pull Request - State: closed - Opened by aschroed almost 3 years ago - 2 comments

#69 - Add n2t for user pfs

Pull Request - State: closed - Opened by aschroed almost 3 years ago

#68 - Extra files release bug fix

Pull Request - State: closed - Opened by andreacosolo almost 3 years ago

#67 - New wf settings

Pull Request - State: closed - Opened by clarabakker about 3 years ago - 1 comment

#66 - Bump bleach from 3.2.1 to 3.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#65 - Bump notebook from 6.1.6 to 6.4.1

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#64 - Bump pygments from 2.7.3 to 2.7.4

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#63 - Bump urllib3 from 1.26.2 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#62 - Bump jinja2 from 2.11.2 to 2.11.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#61 - Bump pywin32 from 300 to 301

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#60 - Add 2 existing pf

Pull Request - State: closed - Opened by aschroed about 3 years ago

#59 - skip patching if values are the same

Pull Request - State: closed - Opened by andreacosolo about 3 years ago

#58 - More geo nb edits

Pull Request - State: closed - Opened by andreacosolo about 3 years ago

#57 - Update release notebook to check for individual with protected_data=True

Pull Request - State: closed - Opened by andreacosolo about 3 years ago - 1 comment

#56 - Updates on the GEO notebook

Pull Request - State: closed - Opened by andreacosolo about 3 years ago

#55 - small fix for case where static_sections property exists but the valu…

Pull Request - State: closed - Opened by aschroed over 3 years ago

#54 - Geo submission updates

Pull Request - State: closed - Opened by andreacosolo over 3 years ago

#53 - Geo submission updates

Pull Request - State: closed - Opened by andreacosolo over 3 years ago

#52 - Patch other fields (release script)

Pull Request - State: closed - Opened by andreacosolo over 3 years ago

#51 - Updates + bug fix for the GEO notebook

Pull Request - State: closed - Opened by andreacosolo over 3 years ago

#50 - Upd rel of extfiles

Pull Request - State: closed - Opened by aschroed over 3 years ago - 1 comment

#49 - Encode wfr updates

Pull Request - State: closed - Opened by KorayKirli over 3 years ago - 1 comment

#48 - alternative script to update files and linked items in opf collections

Pull Request - State: closed - Opened by aschroed almost 4 years ago

#47 - opf status notebook: bug fix + documentation improved

Pull Request - State: closed - Opened by andreacosolo almost 4 years ago

#46 - add notebook to change status of an opf collection

Pull Request - State: closed - Opened by andreacosolo almost 4 years ago

#45 - Added github action for CI and publish; removed travis.yml

Pull Request - State: closed - Opened by aschroed almost 4 years ago

#44 - Geo submission

Pull Request - State: closed - Opened by andreacosolo almost 4 years ago - 1 comment

#43 - updated dcicutil dependency to be >= 1.2.1

Pull Request - State: closed - Opened by aschroed about 4 years ago

#42 - hic_table.py Markdown Table Option Added

Pull Request - State: closed - Opened by utku-ozturk about 4 years ago

#41 - rebuild poetry

Pull Request - State: closed - Opened by KorayKirli about 4 years ago

#40 - bug fix

Pull Request - State: closed - Opened by andreacosolo about 4 years ago

#39 - enzymes

Pull Request - State: closed - Opened by KorayKirli over 4 years ago

#38 - Updated to more generic form of parse_damid script

Pull Request - State: closed - Opened by aschroed over 4 years ago

#37 - Add publish

Pull Request - State: closed - Opened by aschroed over 4 years ago

#36 - Test fix local files

Pull Request - State: closed - Opened by sbreiff over 4 years ago

#35 - Hi-C summary table

Pull Request - State: closed - Opened by andreacosolo over 4 years ago - 1 comment

#34 - Wr poetry

Pull Request - State: closed - Opened by aschroed over 4 years ago

#33 - Script to create Hi-C summary table

Pull Request - State: closed - Opened by andreacosolo over 4 years ago - 1 comment

#32 - edited geo2fdn script to add SRX dbxref to experiments

Pull Request - State: closed - Opened by sbreiff over 4 years ago

#31 - version update

Pull Request - State: closed - Opened by KorayKirli over 4 years ago

#30 - Releasing HeLa-related files

Pull Request - State: closed - Opened by andreacosolo over 4 years ago - 1 comment

#29 - last minute fixes

Pull Request - State: closed - Opened by andreacosolo almost 5 years ago

#28 - rename accession and uuid

Pull Request - State: closed - Opened by andreacosolo almost 5 years ago

#27 - Update to replace sets

Pull Request - State: closed - Opened by andreacosolo almost 5 years ago

#26 - Cleanup notebooks

Pull Request - State: closed - Opened by KorayKirli almost 5 years ago

#25 - Test fixes

Pull Request - State: closed - Opened by sbreiff almost 5 years ago

#24 - Bamqc update

Pull Request - State: closed - Opened by andreacosolo almost 5 years ago

#23 - Microscopy template updates

Pull Request - State: closed - Opened by KorayKirli over 5 years ago - 1 comment

#22 - added a few more autofilled fields in microscopy template nb

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

#21 - Tweak rep replace

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

#20 - Pre commit

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

#19 - nb updates

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

#18 - Tweak find and release

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

#17 - moved script_utils to functions folder

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

#16 - Geo bs fix

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

#15 - Geo2fdn biosampleedits

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

#14 - Geo2fdn fixes

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

GitHub / 4dn-dcic/dcicwrangling issues and pull requests