Fixed testing, rebased

This commit is contained in:
sruthipsuresh 2021-01-28 14:38:32 -06:00
parent e360617ac6
commit 84b66e4f38
7 changed files with 24 additions and 240 deletions

24
.github/filters.yml vendored
View file

@ -144,3 +144,27 @@ trimgalore:
ucsc_bedgraphtobigwig: ucsc_bedgraphtobigwig:
- software/ucsc/bedgraphtobigwig/** - software/ucsc/bedgraphtobigwig/**
- tests/software/ucsc/bedgraphtobigwig/** - tests/software/ucsc/bedgraphtobigwig/**
bedtools_complement:
- software/bedtools/complement/**
- tests/software/bedtools/**
bedtools_genomecov:
- software/bedtools/genomecov/**
- tests/software/bedtools/**
bedtools_intersect:
- software/bedtools/intersect/**
- tests/software/bedtools/**
bedtools_merge:
- software/bedtools/merge/**
- tests/software/bedtools/**
bedtools_slop:
- software/bedtools/slop/**
- tests/software/bedtools/**
bedtools_sort:
- software/bedtools/sort/**
- tests/software/bedtools/**

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@ -1,40 +0,0 @@
name: bedtools_complement
on:
push:
paths:
- software/bedtools/complement/**
- .github/workflows/bedtools_complement.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/complement/**
- .github/workflows/bedtools_complement.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_complement --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bedtools_genomecov
on:
push:
paths:
- software/bedtools/genomecov/**
- .github/workflows/bedtools_genomecov.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/genomecov/**
- .github/workflows/bedtools_genomecov.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_genomecov --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bedtools_intersect
on:
push:
paths:
- software/bedtools/intersect/**
- .github/workflows/bedtools_intersect.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/intersect/**
- .github/workflows/bedtools_intersect.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_intersect --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bedtools_merge
on:
push:
paths:
- software/bedtools/merge/**
- .github/workflows/bedtools_merge.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/merge/**
- .github/workflows/bedtools_merge.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_merge --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bedtools_slop
on:
push:
paths:
- software/bedtools/slop/**
- .github/workflows/bedtools_slop.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/slop/**
- .github/workflows/bedtools_slop.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_slop --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bedtools_sort
on:
push:
paths:
- software/bedtools/sort/**
- .github/workflows/bedtools_sort.yml
- tests/software/bedtools/**
pull_request:
paths:
- software/bedtools/sort/**
- .github/workflows/bedtools_sort.yml
- tests/software/bedtools/**
jobs:
ci_test:
runs-on: ubuntu-latest
strategy:
matrix:
nxf_version: [20.11.0-edge]
env:
NXF_ANSI_LOG: false
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
env:
NXF_VER: ${{ matrix.nxf_version }}
run: |
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 bedtools_sort --symlink --wt 2