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change cache restore step id
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@ktmeaton
ktmeaton committed Jul 24, 2020
1 parent 9b9aaff commit c1c102b
Showing 1 changed file with 31 additions and 46 deletions.
77 changes: 31 additions & 46 deletions .github/workflows/ci.yaml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
#------------------------------------------------------------------------------#
name: Continuous Integration

#------------------------------------------------------------------------------#
# Global workflow environment variables
env:
EAGER_CONDA_ENV: "nf-core-eager-2.2.0dev"
Expand All @@ -10,30 +11,29 @@ env:
CONDA_PKGS_DIRS: "/home/runner/miniconda/pkgs"
NF_VER: "20.01.0"
AUSPICE_VER: "2.17.0"

#------------------------------------------------------------------------------#
# Workflow conditions
on:
push:
branches:
- '*'
- 'master'
paths:
- '.github/workflows/ci.yaml'
- 'environment.yaml'

#------------------------------------------------------------------------------#
jobs:
#----------------------------------------------------------------------------#
# Dependency Installation #
#----------------------------------------------------------------------------#
# Install dependencies
install :
runs-on: ubuntu-latest
steps:
#------------------------------------------------------------------------#
# Install nextflow
- name: install nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
#------------------------------------------------------------------------#
# Acquire env files and src code #
#------------------------------------------------------------------------#
# download nextflow pipelines
- name: download nf-core/eager
shell: bash -l {0}
Expand All @@ -44,6 +44,7 @@ jobs:
# Move env file into github workspace for hashing
cp ~/.nextflow/assets/nf-core/eager/environment.yml \
./nf-core-eager.yaml
- name: download ktmeaton/plague-phylogeography
shell: bash -l {0}
run: |
Expand All @@ -56,31 +57,26 @@ jobs:
cp ~/.nextflow/assets/ktmeaton/plague-phylogeography/config/nextstrain.yaml \
./nextstrain.yaml
#------------------------------------------------------------------------#
# Restore (cache) conda environments #
#------------------------------------------------------------------------#
# Setup conda
# Restore (cache) conda environments
- name: setup conda
uses: goanpeca/setup-miniconda@v1
# Restore (and later cache) the nf-core/eager conda env
# Only if the environment yaml file changed

- name: cache eager env
uses: actions/cache@v2
id: eager-env-cache
with:
path: |
/home/runner/miniconda/envs/nf-core-eager-2.2.0dev
key: eager-env-cache-${{ runner.os }}-test2-${{ hashFiles('./nf-core-eager.yaml') }}
# Restore (and later cache) the plague-phylogeography conda env
# Only if the environment yaml file changed

- name: cache plague-phylogeography env
uses: actions/cache@v2
id: plague-phylogeography-env-cache
with:
path: |
/home/runner/miniconda/envs/plague-phylogeography-0.1.4dev
key: plague-phylogeography-env-cache-${{ runner.os }}-test2-${{ hashFiles('./ktmeaton-plague-phylogeography.yaml') }}
# Restore (and later cache) the nextstrain conda env
# Only if the nextstrain yaml file changed

- name: cache nextstrain env
uses: actions/cache@v2
id: nextstrain-env-cache
Expand All @@ -90,23 +86,21 @@ jobs:
key: nextstrain-env-cache-${{ runner.os }}-test2-${{ hashFiles('./nextstrain.yaml') }}

#------------------------------------------------------------------------#
# Create conda environments #
#------------------------------------------------------------------------#
# create eager env
# create conda environments (if not restored)
- name: create nf-core/eager env
if: steps.eager-env-cache.outputs.cache-hit != 'true'
shell: bash -l {0}
run: |
conda env create -f ~/.nextflow/assets/nf-core/eager/environment.yml
conda install -n ${EAGER_CONDA_ENV} -c bioconda nextflow==${NF_VER}
conda install -n ${EAGER_CONDA_ENV} -c anaconda graphviz
# Create plague-phylogeography env
- name: create ktmeaton/plague-phylogeography env
if: steps.plague-phylogeography-env-cache.outputs.cache-hit != 'true'
shell: bash -l {0}
run: |
conda env create -f ~/.nextflow/assets/ktmeaton/plague-phylogeography/environment.yaml
# Create nextstrain env
- name: create nextstrain env
if: steps.nextstrain-env-cache.outputs.cache-hit != 'true'
shell: bash -l {0}
Expand All @@ -116,25 +110,23 @@ jobs:
npm install --global auspice@${AUSPICE_VER}
conda deactivate
#------------------------------------------------------------------------#
# Test conda environments #
#------------------------------------------------------------------------#
# test eager env
# Test conda environments
- name: test eager env
shell: bash -l {0}
run: |
conda activate ${EAGER_CONDA_ENV}
which nextflow
nextflow -v
conda deactivate
# test plague-phylogeography env
- name: test plague-phylogeography env
shell: bash -l {0}
run: |
conda activate ${PHYLO_CONDA_ENV}
which nextflow
nextflow -v
conda deactivate
# test nextstrain env
- name: test nextstrain env
shell: bash -l {0}
run: |
Expand All @@ -148,32 +140,27 @@ jobs:
conda deactivate
#----------------------------------------------------------------------------#
# Assembled Genome Test #
#----------------------------------------------------------------------------#
# Assembled Genome Test
assembly:
needs: install
runs-on: ubuntu-latest
steps:
#------------------------------------------------------------------------#
# Restore (cache) conda environments #
#------------------------------------------------------------------------#
# Setup conda
# Restore (cache) conda environments
- name: setup conda
uses: goanpeca/setup-miniconda@v1
# Restore the plague-phylogeography conda env
- name: cache plague-phylogeography env

- name: restore plague-phylogeography env
uses: actions/cache@v2
id: plague-phylogeography-env-cache
id: plague-phylogeography-env-cache-restore
with:
path: |
/home/runner/miniconda/envs/plague-phylogeography-0.1.4dev
key: plague-phylogeography-env-cache-${{ runner.os }}-test2-${{ hashFiles('./ktmeaton-plague-phylogeography.yaml') }}
#------------------------------------------------------------------------#
# Test Pipeline #
#------------------------------------------------------------------------#
# Run Assembly Pipeline (only if cache restored)
# Test Pipeline
- name: assembly pipeline
if: steps.plague-phylogeography-env-cache.outputs.cache-hit == 'true'
if: steps.plague-phylogeography-env-cache-restore.outputs.cache-hit == 'true'
shell: bash -l {0}
run: |
conda activate ${PHYLO_CONDA_ENV}
Expand All @@ -184,33 +171,31 @@ jobs:
--skip_outgroup_download \
--outdir test
#------------------------------------------------------------------------#
# Artifact Upload #
#------------------------------------------------------------------------#
# Sqlite Import
# Artifact Upload
- name: artifact sqlite-import
uses: actions/upload-artifact@v2
with:
name: sqlite-import
path: test/sqlite_import/
# Snippy Pairwise

- name: artifact snippy-pairwise
uses: actions/upload-artifact@v2
with:
name: snippy-pairwise
path: test/snippy_pairwise/output10X/
# IQTREE

- name: artifact iqtree
uses: actions/upload-artifact@v2
with:
name: iqtree
path: test/iqtree/
# MultiQC

- name: artifact multiqc
uses: actions/upload-artifact@v2
with:
name: multiqc
path: test/multiqc/multiqc_report.html
# Trace

- name: artifact trace
uses: actions/upload-artifact@v2
with:
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