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Exploration notebook for creating a reference of consensus labels #936

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merged 19 commits into from
Dec 18, 2024
Merged

Exploration notebook for creating a reference of consensus labels #936

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d58c028
Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/on…
allyhawkins Dec 6, 2024
9f10320
add LCA to dictionary
allyhawkins Dec 12, 2024
770c1c8
consensus labels from references notebook
allyhawkins Dec 12, 2024
6aa406b
add some headers for tables
allyhawkins Dec 12, 2024
6e9a611
rendered notebook
allyhawkins Dec 12, 2024
c011170
update lockfile
allyhawkins Dec 12, 2024
27dc591
Start running cell-type-consensus module CI workflows
jaclyn-taroni Dec 16, 2024
6357a44
Add cell-type-consensus to workflows pertaining to all modules
jaclyn-taroni Dec 16, 2024
e14f6a3
Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/on…
allyhawkins Dec 17, 2024
7f65e64
test updating lock file
allyhawkins Dec 17, 2024
66cfcf5
Apply suggestions from code review
allyhawkins Dec 17, 2024
0e89309
keep myeloid and epithelial
allyhawkins Dec 17, 2024
80264bd
run GHA on docker image
allyhawkins Dec 17, 2024
991be1d
Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/on…
allyhawkins Dec 17, 2024
2fab7a5
Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/on…
allyhawkins Dec 17, 2024
98eb9df
install awscli
allyhawkins Dec 17, 2024
f1d165c
formatting
allyhawkins Dec 17, 2024
e3ad414
spell part
allyhawkins Dec 18, 2024
3676e8d
add note about keratinocytes
allyhawkins Dec 18, 2024
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1 change: 1 addition & 0 deletions .github/components/dictionary.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,7 @@ Jitter
JSON
Jupyter
karyotyping
LCA
leiden
LGBTQ
licensor
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1 change: 1 addition & 0 deletions .github/workflows/docker_all-modules.yml
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Expand Up @@ -42,6 +42,7 @@ jobs:
- cell-type-wilms-tumor-14
- cell-type-nonETP-ALL-03
- cell-type-ETP-ALL-03
- cell-type-consensus
uses: ./.github/workflows/build-push-docker-module.yml
if: github.repository_owner == 'AlexsLemonade'
with:
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32 changes: 16 additions & 16 deletions .github/workflows/docker_cell-type-consensus.yml
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Expand Up @@ -13,22 +13,22 @@ concurrency:
cancel-in-progress: true

on:
# pull_request:
# branches:
# - main
# paths:
# - "analyses/cell-type-consensus/Dockerfile"
# - "analyses/cell-type-consensus/.dockerignore"
# - "analyses/cell-type-consensus/renv.lock"
# - "analyses/cell-type-consensus/conda-lock.yml"
# push:
# branches:
# - main
# paths:
# - "analyses/cell-type-consensus/Dockerfile"
# - "analyses/cell-type-consensus/.dockerignore"
# - "analyses/cell-type-consensus/renv.lock"
# - "analyses/cell-type-consensus/conda-lock.yml"
pull_request:
branches:
- main
paths:
- "analyses/cell-type-consensus/Dockerfile"
- "analyses/cell-type-consensus/.dockerignore"
- "analyses/cell-type-consensus/renv.lock"
- "analyses/cell-type-consensus/conda-lock.yml"
push:
branches:
- main
paths:
- "analyses/cell-type-consensus/Dockerfile"
- "analyses/cell-type-consensus/.dockerignore"
- "analyses/cell-type-consensus/renv.lock"
- "analyses/cell-type-consensus/conda-lock.yml"
workflow_dispatch:
inputs:
push-ecr:
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4 changes: 4 additions & 0 deletions .github/workflows/run_all-modules.yml
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Expand Up @@ -40,6 +40,9 @@ jobs:
cell-type-nonETP-ALL-03:
uses: ./.github/workflows/run_cell-type-nonETP-ALL-03.yml

cell-type-consensus:
uses: ./.github/workflows/run_cell-type-consensus.yml

## Add additional modules above this comment, and to the needs list below
check-jobs:
if: ${{ always() }}
Expand All @@ -52,6 +55,7 @@ jobs:
- cell-type-wilms-14
- cell-type-ETP-ALL-03
- cell-type-nonETP-ALL-03
- cell-type-consensus
runs-on: ubuntu-latest
steps:
- name: Checkout template file
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18 changes: 9 additions & 9 deletions .github/workflows/run_cell-type-consensus.yml
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Expand Up @@ -19,15 +19,15 @@ concurrency:

on:
workflow_dispatch:
# workflow_call:
# pull_request:
# branches:
# - main
# paths:
# - analyses/cell-type-consensus/**
# - "!analyses/cell-type-consensus/Dockerfile"
# - "!analyses/cell-type-consensus/.dockerignore"
# - .github/workflows/run_cell-type-consensus.yml
workflow_call:
pull_request:
branches:
- main
paths:
- analyses/cell-type-consensus/**
- "!analyses/cell-type-consensus/Dockerfile"
- "!analyses/cell-type-consensus/.dockerignore"
- .github/workflows/run_cell-type-consensus.yml

jobs:
run-module:
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