molonc/sisyphus issues and pull requests

#174 - Bump scipy from 1.1.0 to 1.11.1 in /workflows

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#173 - Bump aiohttp from 3.7.4.post0 to 3.9.4

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#172 - Bump idna from 2.7 to 3.7

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#171 - Bump idna from 2.7 to 3.7 in /workflows

Pull Request - State: open - Opened by dependabot[bot] 6 months ago
Labels: dependencies

#170 - Bump cryptography from 2.2.1 to 42.0.2

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#169 - Bump cryptography from 2.2.1 to 42.0.2 in /workflows

Pull Request - State: open - Opened by dependabot[bot] 8 months ago
Labels: dependencies

#168 - Bump cryptography from 2.2.1 to 42.0.0

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#167 - Bump cryptography from 2.2.1 to 42.0.0 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#166 - Bump aiohttp from 3.7.4.post0 to 3.9.2

Pull Request - State: closed - Opened by dependabot[bot] 8 months ago - 1 comment
Labels: dependencies

#165 - Bump aiohttp from 3.7.4.post0 to 3.9.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#164 - Bump paramiko from 2.4.1 to 3.4.0 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#163 - Bump urllib3 from 1.23 to 1.26.18

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#162 - chore(deps): bump pillow from 8.2.0 to 10.2.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#161 - chore(deps): bump jinja2 from 2.10 to 3.1.3 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#160 - chore(deps): bump jinja2 from 2.10 to 3.1.3

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#159 - chore(deps): bump paramiko from 2.4.1 to 3.4.0

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#158 - chore(deps): bump urllib3 from 1.23 to 1.26.18 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] 9 months ago - 1 comment
Labels: dependencies

#157 - chore(deps): bump certifi from 2019.9.11 to 2022.12.7

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

#156 - chore(deps): bump certifi from 2018.4.16 to 2022.12.7 in /workflows

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

#155 - chore(deps): bump certifi from 2018.11.29 to 2022.12.7 in /datamanagement/miscellaneous/py2hdfread

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

#154 - chore(deps): bump pillow from 8.2.0 to 9.3.0

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

#153 - chore(deps): bump nbconvert from 6.0.7 to 6.5.1

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

#152 - chore(deps): bump nbconvert from 6.0.7 to 6.3.0

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

#151 - chore(deps): bump mistune from 0.8.4 to 2.0.3

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

#150 - chore(deps): bump numpy from 1.17.4 to 1.22.0

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

#149 - chore(deps): bump numpy from 1.15.4 to 1.22.0 in /datamanagement/miscellaneous/py2hdfread

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

#148 - chore(deps): bump numpy from 1.14.5 to 1.22.0 in /workflows

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

#147 - chore(deps): bump notebook from 6.4.0 to 6.4.12

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

#146 - chore(deps): bump pyjwt from 1.7.1 to 2.4.0

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

#145 - chore(deps): bump pyjwt from 1.6.4 to 2.4.0 in /workflows

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

#144 - 2021 bccrc

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

#143 - 2021 bccrc

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

#142 - chore(deps): bump pypdf2 from 1.26.0 to 1.27.5 in /workflows

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

#141 - chore(deps): bump notebook from 6.4.0 to 6.4.10

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

#140 - chore(deps): bump paramiko from 2.6.0 to 2.10.1

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

#139 - chore(deps): bump paramiko from 2.4.1 to 2.10.1 in /workflows

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

#138 - chore(deps): bump pillow from 8.2.0 to 9.0.1

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

#137 - chore(deps): bump ipython from 7.13.0 to 7.16.3

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

#136 - chore(deps): bump pillow from 8.2.0 to 9.0.0

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

#135 - feature: add is_control to metadata.yaml

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

#134 - chore(deps): bump pillow from 8.2.0 to 8.3.2

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

#133 - chore(deps): bump notebook from 6.4.0 to 6.4.1

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

#132 - add 10x download script add jecy to jira assignment

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

#131 - chore(deps): bump urllib3 from 1.25.7 to 1.26.5

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

#130 - chore(deps): bump urllib3 from 1.23 to 1.26.5 in /workflows

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

#129 - chore(deps): bump urllib3 from 1.25.7 to 1.25.8

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

#128 - update exception flag for missing blob

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

#127 - chore(deps): bump pygments from 2.4.2 to 2.7.4

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

#126 - chore(deps): bump pyyaml from 5.1 to 5.4 in /datamanagement/miscellaneous/py2hdfread

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

#125 - chore(deps): bump pyyaml from 5.1.2 to 5.4

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

#124 - chore(deps): bump pyyaml from 3.12 to 5.4 in /workflows

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

#123 - chore(deps): bump jinja2 from 2.10.3 to 2.11.3

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

#122 - chore(deps): bump jinja2 from 2.10 to 2.11.3 in /workflows

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

#121 - updated requirement azure-storage-blob==12.8.0b1 is essential

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

#120 - pytesting for dbclients.tantalus

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

#119 - chore(deps): bump jinja2 from 2.10 to 2.10.1 in /workflows

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

#118 - feature: overwrite option for transfer dataset

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

#117 - dbclient: updated azure client code

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

#116 - Update jira_utils.py

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

#115 - added jpham's weekly reporting script

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

#114 - chore(deps): bump cryptography from 2.8 to 3.2

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#113 - chore(deps): bump cryptography from 2.2.1 to 3.2 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#112 - refactor: tenx importing and pipeline automation

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

#111 - chore: check inputs exist + other minor changes

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

#110 - chore(deps): bump urllib3 from 1.23 to 1.24.2 in /workflows

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago - 1 comment
Labels: dependencies

#109 - Transferfilesfix

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

#108 - Addfastqmetadata

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

#107 - datamanagement: rename dlp fastqs

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

#106 - templates: reworked fastqs filenames

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

#105 - Fixhapscells

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

#104 - bugfix: cell inputs for haplotype calling

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

#103 - update: spectrum normal ids

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

#102 - bugfix: background image fixes

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

#101 - feature: microscope preprocessing analysis

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

#100 - chore: run pseudobulk after qc

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

#99 - Bugfix and Add new features

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

#98 - update: cellenone scripts

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

#97 - refactor: cli unified and naming from args not datasets

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

#96 - Azcopytransfer

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

#95 - chore: script to split qc analyses on tantalus

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

#94 - temp: recalculate is_contaminated

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

#93 - feature: get most recent of multiple datasets

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

#92 - TANTA-270: add jira ticket to name template of dlp bam sequence datasets

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

#91 - SISY-184: remove cell filtering for snv_genotyping and allele_counting

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

#90 - TANTA-271: updated naming template for dlp results

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

#89 - Normalascells

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

#88 - refactor: trigger qc runs

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

#87 - Scdna347

Pull Request - State: closed - Opened by eliko1991 over 4 years ago

#86 - Scdna347

Pull Request - State: closed - Opened by eliko1991 over 4 years ago

#85 - Qc prod

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

#84 - fastq metadata generator

Pull Request - State: closed - Opened by eliko1991 over 4 years ago

#83 - refactor: annotation, hmmcopy, alignment now in new class structure

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

#82 - Pseudobulktestdatasetfixup

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

#81 - Splitwgsauto

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

#80 - refactor: change bams directory

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

#79 - Singlelibpseudobulk

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

#78 - Add ability to load a single dataset

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

#77 - build(deps): bump paramiko from 2.4.1 to 2.4.2 in /workflows

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

#76 - build(deps): bump requests from 2.19.1 to 2.20.0 in /workflows

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

#75 - build(deps): bump cryptography from 2.2.1 to 2.3 in /workflows

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

GitHub / molonc/sisyphus issues and pull requests