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Added support for multiple samples in raw/ (#540) #516

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Added support for multiple samples in raw/ (#540)

Added support for multiple samples in raw/ (#540) #516

Workflow file for this run

.github/workflows/ci.yml at 7407281
name: CI
# Controls when the action will run.
on:
# Triggers the workflow on push or pull request events but only for the master branch
push:
branches: [ master ]
paths-ignore:
- README.md
- CHANGES.md
- .gitpod.yml
- 'docs/**'
- 'setup/**'
- 'env/*'
pull_request:
branches: [ master ]
paths-ignore:
- README.md
- CHANGES.md
- .gitpod.yml
- 'docs/**'
- 'setup/**'
- 'env/*'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
jobs:
# Downloads exemplar data from S3 as needed
setup:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Install Nextflow
run: curl -fsSL get.nextflow.io | bash
# Exemplars will be cached
- name: Exemplar-001 cache
uses: actions/cache@v3
id: cache-ex001
with:
path: ~/data/exemplar-001
key: ex001-2022-02-24
- name: Exemplar-001 (w/ autofluorescence) cache
uses: actions/cache@v3
id: cache-ex001-af
with:
path: ~/data/af/exemplar-001
key: ex001-af-2023-01-14
- name: Exemplar-002 cache
uses: actions/cache@v3
id: cache-ex002
with:
path: ~/data/exemplar-002
key: ex002-2022-02-24
# Download data only if no cache is available
- name: Exemplar-001 download
if: steps.cache-ex001.outputs.cache-hit != 'true'
run: ./nextflow exemplar.nf --name exemplar-001 --path ~/data
- name: Exemplar-001 (w/ autofluorescence) download
if: steps.cache-ex001-af.outputs.cache-hit != 'true'
run: ./nextflow exemplar.nf --name exemplar-001 --path ~/data/af --from-cycle 1 --to-cycle 3
- name: Exemplar-002 download
if: steps.cache-ex002.outputs.cache-hit != 'true'
run: ./nextflow exemplar.nf --name exemplar-002 --path ~/data --from-cycle 6 --to-cycle 7
# Test exemplar-001
ex001:
strategy:
matrix:
params:
- --viz
- --start-at illumination --stop-at registration
- --background
- --background --background-method imagej-rolling-ball
- --segmentation cypository --cypository-opts '--channel 10 --scalingFactor 2' --s3seg-opts '--logSigma 45 300'
- --segmentation ilastik,mesmer
- --segmentation cellpose --mcquant-opts '--masks *masks.tif'
- --viz --segmentation ilastik -profile singularity
needs: setup
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Install Singularity
uses: eWaterCycle/setup-singularity@v7
if: ${{ contains(matrix.params, 'singularity') }}
with:
singularity-version: 3.8.3
- name: Install Nextflow
run: curl -fsSL get.nextflow.io | bash
- name: Restore exemplar-001 cache
uses: actions/cache@v3
if: ${{ !contains(matrix.params, 'background') }}
with:
path: ~/data/exemplar-001
key: ex001-2022-02-24
- name: Restore exemplar-001 (w/ autofluorescence) cache
uses: actions/cache@v3
if: ${{ contains(matrix.params, 'background') }}
with:
path: ~/data/af/exemplar-001
key: ex001-af-2023-01-14
- name: Adjust data location for the autofluorescence exemplar
if: ${{ contains(matrix.params, 'background') }}
run: mv ~/data/af/exemplar-001 ~/data
- name: Test exemplar-001 with additional parameters
run: |
docker rmi -f $(docker images -a -q)
./nextflow main.nf --in ~/data/exemplar-001 ${{ matrix.params }}
ls -R ~/data/exemplar-001
- name: Upload processed result
uses: actions/upload-artifact@v2
if: ${{ github.event_name == 'push' && contains(matrix.params, 'viz') }}
with:
name: exemplar-001
path: |
~/data/exemplar-001
!~/data/exemplar-001/raw
!~/data/exemplar-001/illumination
# Step-by-step test of exemplar-001
ex001-by-step:
needs: setup
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Install Nextflow
run: curl -fsSL get.nextflow.io | bash
- name: Restore exemplar-001 cache
uses: actions/cache@v3
with:
path: ~/data/exemplar-001
key: ex001-2022-02-24
- name: Test exemplar-001 step-by-step
run: |
docker rmi -f $(docker images -a -q)
./nextflow main.nf --in ~/data/exemplar-001 --start-at registration --stop-at registration
./nextflow clean -f last
./nextflow main.nf --in ~/data/exemplar-001 --start-at segmentation --stop-at segmentation
./nextflow main.nf --in ~/data/exemplar-001 --start-at watershed --stop-at watershed
./nextflow main.nf --in ~/data/exemplar-001 --start-at quantification --stop-at quantification
docker rmi -f $(docker images -a -q)
./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream scimap
./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream naivestates
./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream fastpg
./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream scanpy
./nextflow main.nf --in ~/data/exemplar-001 --start-at downstream --stop-at downstream --downstream flowsom
ls -R ~/data/exemplar-001
# One-shot test of exemplar-002
ex002:
needs: setup
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Install Nextflow
run: curl -fsSL get.nextflow.io | bash
- name: Restore exemplar-002 cache
uses: actions/cache@v3
with:
path: ~/data/exemplar-002
key: ex002-2022-02-24
- name: Test exemplar-002
run: |
docker rmi -f $(docker images -a -q)
./nextflow main.nf --in ~/data/exemplar-002 --tma --start-at registration --stop-at segmentation
docker rmi -f $(docker images -a -q)
./nextflow main.nf --in ~/data/exemplar-002 --tma --start-at quantification
ls -R ~/data/exemplar-002