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ci: Get rid of software folder

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Edmund Miller 2020-12-01 11:40:16 -06:00
parent 6404c3390d
commit 65697532a1
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12 changed files with 56 additions and 56 deletions
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36
.github/workflows/bwa_index.yml vendored Normal file
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@ -0,0 +1,36 @@
name: bwa_index
on:
push:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests/software/bwa/**
pull_request:
paths:
- software/bwa/index/**
- .github/workflows/bwa_index.yml
- tests/software/bwa/**
jobs:
ci_test:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
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
# Test the module
- run: pytest --tag bwa_index --symlink --wt 2

4
.github/workflows/software/bwa_mem.yml → .github/workflows/bwa_mem.yml vendored
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@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/bwa/mem/** - software/bwa/mem/**
- .github/workflows/software/bwa_mem.yml - .github/workflows/bwa_mem.yml
- tests/software/bwa/** - tests/software/bwa/**
pull_request: pull_request:
paths: paths:
- software/bwa/mem/** - software/bwa/mem/**
- .github/workflows/software/bwa_mem.yml - .github/workflows/bwa_mem.yml
- tests/software/bwa/** - tests/software/bwa/**
jobs: jobs:

4
.github/workflows/software/picard_collectmultiplemetrics.yml → .github/workflows/picard_collectmultiplemetrics.yml vendored
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@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/picard/collectmultiplemetrics/** - software/picard/collectmultiplemetrics/**
- .github/workflows/software/picard_collectmultiplemetrics.yml - .github/workflows/picard_collectmultiplemetrics.yml
- tests/software/picard/** - tests/software/picard/**
pull_request: pull_request:
paths: paths:
- software/picard/collectmultiplemetrics/** - software/picard/collectmultiplemetrics/**
- .github/workflows/software/picard_collectmultiplemetrics.yml - .github/workflows/picard_collectmultiplemetrics.yml
- tests/software/picard/** - tests/software/picard/**
jobs: jobs:

4
.github/workflows/software/picard_markduplicates.yml → .github/workflows/picard_markduplicates.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/picard/markduplicates/** - software/picard/markduplicates/**
- .github/workflows/software/picard_markduplicates.yml - .github/workflows/picard_markduplicates.yml
- tests/software/picard/** - tests/software/picard/**
pull_request: pull_request:
paths: paths:
- software/picard/markduplicates/** - software/picard/markduplicates/**
- .github/workflows/software/picard_markduplicates.yml - .github/workflows/picard_markduplicates.yml
- tests/software/picard/** - tests/software/picard/**
jobs: jobs:

4
.github/workflows/software/picard_mergesamfiles.yml → .github/workflows/picard_mergesamfiles.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/picard/mergesamfiles/** - software/picard/mergesamfiles/**
- .github/workflows/software/picard_mergesamfiles.yml - .github/workflows/picard_mergesamfiles.yml
- tests/software/picard/** - tests/software/picard/**
pull_request: pull_request:
paths: paths:
- software/picard/mergesamfiles/** - software/picard/mergesamfiles/**
- .github/workflows/software/picard_mergesamfiles.yml - .github/workflows/picard_mergesamfiles.yml
- tests/software/picard/** - tests/software/picard/**
jobs: jobs:

4
.github/workflows/software/samtools_flagstat.yml → .github/workflows/samtools_flagstat.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/samtools/flagstat/** - software/samtools/flagstat/**
- .github/workflows/software/samtools_flagstat.yml - .github/workflows/samtools_flagstat.yml
- tests/software/samtools/** - tests/software/samtools/**
pull_request: pull_request:
paths: paths:
- software/samtools/flagstat/** - software/samtools/flagstat/**
- .github/workflows/software/samtools_flagstat.yml - .github/workflows/samtools_flagstat.yml
- tests/software/samtools/** - tests/software/samtools/**
jobs: jobs:

4
.github/workflows/software/samtools_idxstats.yml → .github/workflows/samtools_idxstats.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/samtools/idxstats/** - software/samtools/idxstats/**
- .github/workflows/software/samtools_idxstats.yml - .github/workflows/samtools_idxstats.yml
- tests/software/samtools/** - tests/software/samtools/**
pull_request: pull_request:
paths: paths:
- software/samtools/idxstats/** - software/samtools/idxstats/**
- .github/workflows/software/samtools_idxstats.yml - .github/workflows/samtools_idxstats.yml
- tests/software/samtools/** - tests/software/samtools/**
jobs: jobs:

4
.github/workflows/software/samtools_index.yml → .github/workflows/samtools_index.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/samtools/index/** - software/samtools/index/**
- .github/workflows/software/samtools_index.yml - .github/workflows/samtools_index.yml
- tests/software/samtools/** - tests/software/samtools/**
pull_request: pull_request:
paths: paths:
- software/samtools/index/** - software/samtools/index/**
- .github/workflows/software/samtools_index.yml - .github/workflows/samtools_index.yml
- tests/software/samtools/** - tests/software/samtools/**
jobs: jobs:

4
.github/workflows/software/samtools_sort.yml → .github/workflows/samtools_sort.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/samtools/sort/** - software/samtools/sort/**
- .github/workflows/software/samtools_sort.yml - .github/workflows/samtools_sort.yml
- tests/software/samtools/** - tests/software/samtools/**
pull_request: pull_request:
paths: paths:
- software/samtools/sort/** - software/samtools/sort/**
- .github/workflows/software/samtools_sort.yml - .github/workflows/samtools_sort.yml
- tests/software/samtools/** - tests/software/samtools/**
jobs: jobs:

4
.github/workflows/software/samtools_stats.yml → .github/workflows/samtools_stats.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/samtools/stats/** - software/samtools/stats/**
- .github/workflows/software/software/samtools_stats.yml - .github/workflows/software/samtools_stats.yml
- tests/software/samtools/** - tests/software/samtools/**
pull_request: pull_request:
paths: paths:
- software/samtools/stats/** - software/samtools/stats/**
- .github/workflows/software/software/samtools_stats.yml - .github/workflows/software/samtools_stats.yml
- tests/software/samtools/** - tests/software/samtools/**
jobs: jobs:

36
.github/workflows/software/bwa_index.yml vendored
View file

@ -1,36 +0,0 @@
name: bwa_index
on:
push:
paths:
- software/bwa/index/**
- .github/workflows/software/bwa_index.yml
- tests/software/bwa/**
pull_request:
paths:
- software/bwa/index/**
- .github/workflows/software/bwa_index.yml
- tests/software/bwa/**
jobs:
ci_test:
runs-on: ubuntu-latest
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
run: |
export NXF_VER="20.07.1"
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
# Test the module
- run: pytest --tag bwa_index --symlink --wt 2

4
.github/workflows/software/trimgalore.yml → .github/workflows/trimgalore.yml vendored
View file

@ -3,12 +3,12 @@ on:
push: push:
paths: paths:
- software/trimgalore/** - software/trimgalore/**
- .github/workflows/software/trimgalore.yml - .github/workflows/trimgalore.yml
- tests/software/trimgalore/** - tests/software/trimgalore/**
pull_request: pull_request:
paths: paths:
- software/trimgalore/** - software/trimgalore/**
- .github/workflows/software/trimgalore.yml - .github/workflows/trimgalore.yml
- tests/software/trimgalore/** - tests/software/trimgalore/**
jobs: jobs: