Ecosyste.ms: Issues

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GitHub / populationgenomics/cpg-utils issues and pull requests

#173 - Add sonarqube scan to test workflow

Pull Request - State: open - Opened by violetbrina 17 days ago

#172 - Add dataproc ip address flag

Pull Request - State: closed - Opened by illusional about 2 months ago - 1 comment

#171 - Bump Hail version in dataproc.py to 0.2.132

Pull Request - State: closed - Opened by jmarshall 2 months ago

#169 - Relaxing pinning to botocore.

Pull Request - State: closed - Opened by milo-hyben 5 months ago - 2 comments

#168 - Update workflow options for cromwell gcs batch

Pull Request - State: closed - Opened by illusional 5 months ago - 1 comment

#167 - Add Hail Default version for Dataproc

Pull Request - State: closed - Opened by MattWellie 5 months ago - 1 comment

#166 - Accept Path as well as str in read_input() and read_input_group()

Pull Request - State: open - Opened by jmarshall 5 months ago - 3 comments

#165 - Abort overlong jobs

Pull Request - State: closed - Opened by MattWellie 5 months ago - 2 comments

#164 - Use basicConfig setup for logging.info messages

Pull Request - State: closed - Opened by MattWellie 6 months ago - 2 comments

#163 - Bash transcribed scripts are rubbish

Issue - State: open - Opened by MattWellie 6 months ago

#162 - Logging patch

Pull Request - State: closed - Opened by MattWellie 6 months ago - 1 comment

#161 - Environment Lock

Pull Request - State: closed - Opened by nevoodoo 6 months ago - 2 comments

#159 - Fix dataproc temp bucket

Pull Request - State: closed - Opened by EddieLF 6 months ago - 1 comment

#158 - Fix dataproc startup (temp folder)

Pull Request - State: closed - Opened by MattWellie 6 months ago - 2 comments

#157 - Dataproc startup borked - trailing slash

Issue - State: closed - Opened by MattWellie 6 months ago - 1 comment
Labels: bug

#156 - Don't include dependencies from requirements.txt

Pull Request - State: closed - Opened by illusional 6 months ago - 5 comments

#154 - Convert workflow to use workload identity federation and update actions versions

Pull Request - State: closed - Opened by jmarshall 7 months ago - 1 comment

#153 - Quote here-document delimiters to avoid expansion

Pull Request - State: closed - Opened by jmarshall 7 months ago - 3 comments

#152 - Refactor repository + add tests

Pull Request - State: closed - Opened by illusional 7 months ago - 1 comment

#151 - Allow init_batch overrides in Query_command

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

#150 - Handle Config better

Issue - State: closed - Opened by MattWellie 10 months ago

#149 - Write cloud config and overwrite env variable

Pull Request - State: closed - Opened by MattWellie 10 months ago - 2 comments

#148 - Driver as default bash image

Pull Request - State: closed - Opened by MattWellie 10 months ago - 2 comments

#147 - Add reset_batch method

Pull Request - State: closed - Opened by illusional 10 months ago - 1 comment

#146 - Don't print config content by default

Pull Request - State: closed - Opened by MattWellie 11 months ago - 1 comment

#145 - Migrate get_batch wrapper to cpg-utils

Pull Request - State: closed - Opened by MattWellie 11 months ago

#144 - Restrict docker push to main only

Pull Request - State: closed - Opened by illusional 12 months ago

#143 - Change ar guid to dash

Pull Request - State: closed - Opened by illusional 12 months ago

#142 - Add ar_guid support to cpg-utils

Pull Request - State: closed - Opened by illusional 12 months ago

#140 - OIDC ID token generation

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

#139 - get_google_identity_token fails in OIDC environment

Issue - State: closed - Opened by illusional over 1 year ago

#138 - Add utility method to upload files to Slack

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

#137 - Get components of a GCP path

Pull Request - State: closed - Opened by EddieLF over 1 year ago - 3 comments

#136 - Bump version: 4.13.0 → 4.14.0

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

#135 - Copy Slack utilities from cpg_workflows

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

#134 - Allow specifying dataset for output_path

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

#133 - Remove help message dependency

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

#132 - Update linters

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

#131 - Lowercase members

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

#130 - Update linters

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

#129 - Make printing the configuration optional

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

#128 - Test path generation

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

#126 - Use gs://cpg-common-main/references instead of gs://cpg-references

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

#125 - `fasta_res_group` only points to unmasked reference

Pull Request - State: open - Opened by vladsavelyev almost 2 years ago - 3 comments

#124 - Configs: handy functions to prepend and append; more validation

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

#123 - Update version pin to be consistent with the hail package

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

#121 - Bump version: 4.9.4 → 4.10.0

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

#120 - Fix code in docs, fix typos, lint

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

#119 - Move `workflows` library out into `cpg-workflows`

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

#118 - Fix email scope identifier

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

#117 - Configuring path schemes in TOML

Pull Request - State: closed - Opened by vladsavelyev almost 2 years ago - 14 comments

#116 - Add option for custom reference fasta path (`workflow/ref_fasta`)

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

#115 - When `workflow/output_version` not set, use alignments hash rather than timestamp

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

#114 - Properly check complete `vds` directories existence

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

#113 - Pin sample-metadata

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

#111 - Workflows: Do not support hb.Resource as expected_outputs for stages

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

#110 - Get pedigree in chunks

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

#109 - TOML option to skip reading pedigree

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

#108 - [workflows] inputs: gather errors of missing seq/reads entries

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

#107 - Build docker tagged by git rev, include workflows requirements

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

#105 - Fix Dockerfile

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

#104 - Workflows: inputs: populate participant metadata

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

#103 - Add `cpg_utils` image into config template

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

#102 - Fix merge conflict (fixes CI docker build)

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

#101 - Add `start_query_context`

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

#100 - Add Dockerfile and Docker CI workflow

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

#99 - Make sure `worfklow/last_stages` correctly treated

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

#98 - Renames get_sequences_by_sample_ids to *_for_sample_ids

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

#96 - Default config: remove images/hail and images/sm-api

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

#95 - Cloud Path: recursively create root dir for Local FS

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

#94 - Workflows: less verbose errors about missing sequence and pedigree

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

#93 - Set `sample.cram` and `sample.gvcf` from corresponding analysis entries

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

#91 - Fix ped call

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

#90 - Pass audience / scope when fetching GCP default credentials

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

#89 - datasets -> only_datasets

Pull Request - State: closed - Opened by vivbak almost 2 years ago - 4 comments

#87 - Workflows: add documentation

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

#86 - Remove coloredlogs

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

#85 - Config's `workflow/check_intermediates` controls `can_reuse()`

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

#84 - Add status reporter test

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

#83 - Remove unused "reuse" jobs

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

#82 - Local FS: create parent directories automatically

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

#81 - Bump version: 4.8.0 → 4.8.1: Attempt to fetch default credentials first

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

#80 - Filter samples according to access level

Pull Request - State: closed - Opened by vivbak about 2 years ago - 9 comments

#79 - Revert reference override

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

#78 - Batch: avoid coping configs to remote for dry run

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

#77 - Bump version: Add ability to override default reference

Pull Request - State: closed - Opened by illusional about 2 years ago - 5 comments

#76 - Bump version: 4.6.2 → 4.6.3

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

#75 - Add networkx for DAG, add `workflows/only_stages` parameter

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

#74 - Bump version: 4.6.1 → 4.6.2: Don't set a pool label by default

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