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Pytest workflow #546

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Pytest workflow #546

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d8994eb
test(default): Rewrite with pytest-workflow
edmundmiller Dec 22, 2020
c9b39ca
test(star_salmon): Rewrite with pytest-workflow
edmundmiller Dec 22, 2020
15e053c
test: GITHUB_WORKSPACE => main.nf
edmundmiller Dec 22, 2020
115c82d
test(star_salmon): Use two tags instead of one
edmundmiller Dec 22, 2020
67fb0dc
ci: Fix syntax error
edmundmiller Dec 23, 2020
4da30ab
test(star_rsem): Rewrite to use pytest-workflow
edmundmiller Dec 23, 2020
2c9ed44
test(hisat2): Rewrite to use pytest-workflow
edmundmiller Dec 23, 2020
0c90a56
ci: Fix step names
edmundmiller Dec 23, 2020
b0309d1
chore: Remove TODOs
edmundmiller Dec 23, 2020
8ca995a
test(salmon): Rewrite to use pytest-workflow
edmundmiller Dec 23, 2020
a75c060
test(sra_download): Rewrite to use pytest-workflow
edmundmiller Dec 23, 2020
2015a0a
ci: Fix typo
edmundmiller Dec 23, 2020
afdf853
test: Fix naming so tests get picked up by pytest
edmundmiller Dec 23, 2020
5d42375
ci: Fix another yaml typo
edmundmiller Dec 23, 2020
f0ce755
ci: Keep working-directories of failures
edmundmiller Dec 23, 2020
002df2f
test(sra_download): main => main.nf
edmundmiller Dec 23, 2020
ca49170
ci: Add " around matrix parameters
edmundmiller Dec 23, 2020
e002906
ci: Remove -- in params
edmundmiller Jan 8, 2021
8118452
ci: Remove extra STAR tags
edmundmiller Jan 8, 2021
2bb4389
ci: Add continue on failure to SRA download
edmundmiller Jan 8, 2021
7cea5ad
ci: Remove --symlink
edmundmiller Feb 2, 2021
73e4459
ci: Remove multiple workflow threads
edmundmiller Feb 2, 2021
a76691d
Fix typo
edmundmiller Apr 27, 2021
f45767e
ci: Add local modules workflow
edmundmiller Apr 28, 2021
57a8560
test: Add config infrastructure
edmundmiller Apr 28, 2021
d0c9f37
tests: Add modules config
edmundmiller Apr 28, 2021
8a9d3c7
test: Get cleaver with module data includeConfig
edmundmiller Apr 28, 2021
873fd10
test(quantify_salmon): Add initial test
edmundmiller Apr 28, 2021
885e5a8
style: s/'/"
edmundmiller Jun 4, 2021
a244b54
test: Bump version to 21.04-0
edmundmiller Jun 10, 2021
14bdb5f
chore: Add a note to default tests only supporting docker
edmundmiller Jun 10, 2021
14eaea7
ci: Use parameters in job names
edmundmiller Jun 10, 2021
6ed824f
test(star_salmon): Add missing tests
edmundmiller Jun 10, 2021
a68e9f5
ci: Fix salmon params
edmundmiller Jun 10, 2021
a2d0a37
test(quantify_salmon): Fix path
edmundmiller Jun 10, 2021
f600692
ci: Upload logs on failure
edmundmiller Jun 10, 2021
b0c92e4
test: Load default nextflow.config
edmundmiller Jun 10, 2021
0e8f245
test: Add modules config include back in
edmundmiller Jun 10, 2021
8ee3524
test(star_salmon): Fix tag
edmundmiller Jun 10, 2021
5275ced
test: Remove all ` in test names
edmundmiller Jun 10, 2021
b2aa206
test: Add modules clone step
edmundmiller Jun 10, 2021
5a4fb66
test: Remove -- in test names
edmundmiller Jun 10, 2021
dd96ef5
test(quantify_salmon): Actually call a value
edmundmiller Jun 10, 2021
8a74e46
ci: Update Local modules to triggers
edmundmiller Jun 10, 2021
faa22a6
test(star_salmon): Mark remove_ribo_rna as failing
edmundmiller Jun 10, 2021
40b93de
test(quant_rsem): Add default test
edmundmiller Jun 10, 2021
617773a
test: Mark subworkflows as failing
edmundmiller Jun 11, 2021
32f2ad2
test(default): Add expected files and their md5sums
edmundmiller Jun 11, 2021
9554d2a
Merge remote-tracking branch 'origin/dev' into pytest-workflow
grst Dec 30, 2021
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195 changes: 156 additions & 39 deletions .github/workflows/ci.yml
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Expand Up @@ -23,11 +23,11 @@ jobs:
# Nextflow versions
include:
# Test pipeline minimum Nextflow version
- NXF_VER: '21.10.3'
NXF_EDGE: ''
- NXF_VER: "21.10.3"
NXF_EDGE: ""
# Test latest edge release of Nextflow
- NXF_VER: ''
NXF_EDGE: '1'
- NXF_VER: ""
NXF_EDGE: "1"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -42,29 +42,45 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with default settings
run: pytest --tag default --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-default-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err

star_salmon:
name: Test STAR Salmon with workflow parameters
name: Test STAR Salmon with ${{ matrix.parameters }}
Comment on lines -50 to +66
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Do we need a separate star_salmon for this? Couldn't this just be another entry in the matrix?

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It could be another entry in the matrix, I was thinking this was a good interim to make sure we didn't miss anything in the conversion.

if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
- "--skip_trimming"
- "--gtf false"
- "--star_index false"
- "--transcript_fasta false"
- "--min_mapped_reads 90"
- "--with_umi"
- "--with_umi --skip_trimming"
- "--remove_ribo_rna --skip_qualimap"
- "--bam_csi_index"
- "--save_align_intermeds --save_reference"
- "--featurecounts_group_type false"
- "skip_qc"
- "remove_ribo_rna"
- "skip_trimming"
- "gtf false"
- "star_index false"
- "transcript_fasta"
- "min_mapped_reads 90"
- "with_umi"
- "skip_trimming"
- "bam_csi_index"
- "save_reference"
- "featurecounts_group_type"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -74,19 +90,35 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_salmon ${{ matrix.parameters }}
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with STAR Salmon and ${{ matrix.parameters }}
run: pytest --tag star --tag salmon --tag "${{ matrix.parameters }}" --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-star_salmon-${{ matrix.parameters }}-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err

star_rsem:
name: Test STAR RSEM with workflow parameters
name: Test STAR RSEM with ${{ matrix.parameters }}
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
- "--rsem_index false"
- "skip_qc"
- "rsem_index false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -96,19 +128,35 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with RSEM STAR and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner star_rsem ${{ matrix.parameters }}
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with STAR RSEM and ${{ matrix.parameters }}
run: pytest --tag star --tag rsem --tag "${{ matrix.parameters }}" --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-star_rsem-${{ matrix.parameters }}-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err

hisat2:
name: Test HISAT2 with workflow parameters
name: Test HISAT2 with ${{ matrix.parameters }}
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc"
- "--hisat2_index false"
- "skip_qc"
- "hisat2_index false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -118,19 +166,35 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Run pipeline with HISAT2 and various parameters
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner hisat2 ${{ matrix.parameters }}
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with HISAT2 ${{ matrix.parameters }}
run: pytest --tag hisat2 --tag "${{ matrix.parameters }}" --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-hisat2-${{ matrix.parameters }}-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err

salmon:
name: Test Salmon with workflow parameters
name: Test Salmon with ${{ matrix.parameters }}
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- "--skip_qc --skip_alignment"
- "--salmon_index false --transcript_fasta false"
- "skip_qc skip_alignment"
- "salmon_index false transcript_fasta false"
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
Expand All @@ -140,6 +204,59 @@ jobs:
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline with Salmon and various parameters
run: pytest --tag salmon --tag "${{ matrix.parameters }}" --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-salmon-${{ matrix.parameters }}-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err

sra_download:
name: Test downloading of public data
if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
runs-on: ubuntu-latest
env:
NXF_VER: ${{ matrix.nxf_ver }}
NXF_ANSI_LOG: false
steps:
- name: Check out pipeline code
uses: actions/checkout@v2

- name: Install Nextflow
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --pseudo_aligner salmon ${{ matrix.parameters }}
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.x"
- name: Install dependencies
run: python -m pip install --upgrade pip pytest-workflow

- name: Run pipeline to download public data
continue-on-error: true
run: pytest --tag sra_download --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-sra_download-${{ matrix.nxf_version }}
path: |
/tmp/pytest_workflow_*/*/.nextflow.log
/tmp/pytest_workflow_*/*/log.out
/tmp/pytest_workflow_*/*/log.err
106 changes: 106 additions & 0 deletions .github/workflows/local_modules.yml
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@@ -0,0 +1,106 @@
name: Local Modules pytest-workflow
on:
push:
branches:
- dev
pull_request:
release:
types: [published]

jobs:
changes:
name: Check for changes
runs-on: ubuntu-latest
outputs:
# Expose matched filters as job 'modules' output variable
modules: ${{ steps.filter.outputs.changes }}
steps:
- uses: actions/checkout@v2
- uses: dorny/paths-filter@v2
id: filter
with:
filters: 'tests/config/pytest_software.yml'

test:
runs-on: ubuntu-latest
name: ${{ matrix.tags }} ${{ matrix.profile }} ${{ matrix.nxf_version }}
needs: changes
if: needs.changes.outputs.modules != '[]'
strategy:
fail-fast: false
matrix:
nxf_version: ['21.04.0-edge']
tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
profile: ['docker', 'singularity'] ## 'conda'
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.x'

- uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-

- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: '3.x'

- name: Install Python dependencies
run: python -m pip install --upgrade pip pytest-workflow

- uses: actions/cache@v2
with:
path: /usr/local/bin/nextflow
key: ${{ runner.os }}-nextflow-${{ matrix.nxf_version }}
restore-keys: |
${{ runner.os }}-nextflow-

- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
CAPSULE_LOG: none
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/

- name: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1

- name: Setup miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}

- name: Conda clean
if: matrix.profile == 'conda'
run: conda clean -a

# Test the module
- name: Run pytest-workflow
# only use one thread for pytest-workflow to avoid race condition on conda cache.
run: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof

- name: Upload logs on failure
if: failure()
uses: actions/upload-artifact@v2
with:
name: logs-${{ matrix.tags }}-${{ matrix.profile }}-${{ matrix.nxf_version }}
path: |
/home/runner/pytest_workflow_*/*/.nextflow.log
/home/runner/pytest_workflow_*/*/log.out
/home/runner/pytest_workflow_*/*/log.err