ci: Add filters for new modules

These snuck in after the 506ebe5 was written
This commit is contained in:
Edmund Miller 2021-02-02 15:27:45 -06:00
parent 341fa43ae3
commit 35ac5c5f15
No known key found for this signature in database
GPG key ID: BD387FF7BC10AA9D
17 changed files with 65 additions and 645 deletions

68
.github/filters.yml vendored
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@ -1,10 +1,19 @@
bowtie2_align:
- software/bowtie2/align/**
- software/bowtie2/build/**
- tests/software/bowtie2/**
bowtie2_build:
- software/bowtie2/build/**
- tests/software/bowtie2/**
bowtie_align: bowtie_align:
- software/bowtie/align/** - software/bowtie/align/**
- software/bowtie/index/** - software/bowtie/build/**
- tests/software/bowtie/** - tests/software/bowtie/**
bowtie_index: bowtie_build:
- software/bowtie/index/** - software/bowtie/build/**
- tests/software/bowtie/** - tests/software/bowtie/**
bwa_index: bwa_index:
@ -15,6 +24,22 @@ bwa_mem:
- software/bwa/mem/** - software/bwa/mem/**
- tests/software/bwa/** - tests/software/bwa/**
cutadapt:
- software/cutadapt/**
- tests/software/cutadapt/**
dsh_filterbed:
- software/dsh/filterbed/**
- tests/software/dsh/**
dsh_splitbed:
- software/dsh/splitbed/**
- tests/software/dsh/**
fastp:
- software/fastp/**
- tests/software/fastp/**
fastqc: fastqc:
- software/fastqc/** - software/fastqc/**
- tests/software/fastqc/** - tests/software/fastqc/**
@ -27,6 +52,10 @@ multiqc:
- software/multiqc/** - software/multiqc/**
- tests/software/multiqc/** - tests/software/multiqc/**
pangolin:
- software/pangolin/**
- tests/software/pangolin/**
picard_collectmultiplemetrics: picard_collectmultiplemetrics:
- software/picard/collectmultiplemetrics/** - software/picard/collectmultiplemetrics/**
- tests/software/picard/** - tests/software/picard/**
@ -43,6 +72,18 @@ preseq_lcextrap:
- software/preseq/lcextrap/** - software/preseq/lcextrap/**
- tests/software/preseq/** - tests/software/preseq/**
quast:
- software/quast/**
- tests/software/quast/**
salmon_index:
- software/salmon/index/**
- tests/software/salmon/**
salmon_quant:
- software/salmon/quant/**
- tests/software/salmon/**
samtools_flagstat: samtools_flagstat:
- software/samtools/flagstat/** - software/samtools/flagstat/**
- tests/software/samtools/** - tests/software/samtools/**
@ -55,6 +96,10 @@ samtools_index:
- software/samtools/index/** - software/samtools/index/**
- tests/software/samtools/** - tests/software/samtools/**
samtools_mpileup:
- software/samtools/mpileup/**
- tests/software/samtools/**
samtools_sort: samtools_sort:
- software/samtools/sort/** - software/samtools/sort/**
- tests/software/samtools/** - tests/software/samtools/**
@ -63,6 +108,23 @@ samtools_stats:
- software/samtools/stats/** - software/samtools/stats/**
- tests/software/samtools/** - tests/software/samtools/**
samtools_view:
- software/samtools/view/**
- tests/software/samtools/**
seacr_callpeak:
- software/seacr/callpeak/**
- tests/software/seacr/**
star_align:
- software/star/align/**
- tests/software/star/**
star_genomegenerate:
- software/star/genomegenerate/**
- tests/software/star/**
stringtie: stringtie:
- software/stringtie/** - software/stringtie/**
- tests/software/stringtie/** - tests/software/stringtie/**

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@ -1,42 +0,0 @@
name: bowtie2_align
on:
push:
paths:
- software/bowtie2/align/**
- software/bowtie2/build/**
- .github/workflows/bowtie2_align.yml
- tests/software/bowtie2/**
pull_request:
paths:
- software/bowtie2/align/**
- software/bowtie2/build/**
- .github/workflows/bowtie2_align.yml
- tests/software/bowtie2/**
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 bowtie2_align --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bowtie2_build
on:
push:
paths:
- software/bowtie2/build/**
- .github/workflows/bowtie2_build.yml
- tests/software/bowtie2/**
pull_request:
paths:
- software/bowtie2/build/**
- .github/workflows/bowtie2_build.yml
- tests/software/bowtie2/**
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 bowtie2_build --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: bowtie_build
on:
push:
paths:
- software/bowtie/build/**
- .github/workflows/bowtie_build.yml
- tests/software/bowtie/**
pull_request:
paths:
- software/bowtie/build/**
- .github/workflows/bowtie_build.yml
- tests/software/bowtie/**
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 bowtie_build --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: cutadapt
on:
push:
paths:
- software/cutadapt/**
- .github/workflows/cutadapt.yml
- tests/software/cutadapt/**
pull_request:
paths:
- software/cutadapt/**
- .github/workflows/cutadapt.yml
- tests/software/cutadapt/**
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 cutadapt --symlink --wt 2

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@ -1,40 +0,0 @@
name: dsh_filterbed
on:
push:
paths:
- software/dsh/filterbed/**
- .github/workflows/dsh_filterbed.yml
- tests/software/dsh/**
pull_request:
paths:
- software/dsh/filterbed/**
- .github/workflows/dsh_filterbed.yml
- tests/software/dsh/**
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 dsh_filterbed --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: dsh_splitbed
on:
push:
paths:
- software/dsh/splitbed/**
- .github/workflows/dsh_splitbed.yml
- tests/software/dsh/**
pull_request:
paths:
- software/dsh/splitbed/**
- .github/workflows/dsh_splitbed.yml
- tests/software/dsh/**
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 dsh_splitbed --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: fastp
on:
push:
paths:
- software/fastp/**
- .github/workflows/fastp.yml
- tests
pull_request:
paths:
- software/fastp/**
- .github/workflows/fastp.yml
- tests
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 fastp --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: pangolin
on:
push:
paths:
- software/pangolin/**
- .github/workflows/pangolin.yml
- tests
pull_request:
paths:
- software/pangolin/**
- .github/workflows/pangolin.yml
- tests
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 pangolin --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: quast
on:
push:
paths:
- software/quast/**
- .github/workflows/quast.yml
- tests
pull_request:
paths:
- software/pquast/**
- .github/workflows/quest.yml
- tests
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 quast --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: salmon_index
on:
push:
paths:
- software/salmon/index/**
- .github/workflows/salmon_index.yml
- tests/software/salmon/**
pull_request:
paths:
- software/salmon/index/**
- .github/workflows/salmon_index.yml
- tests/software/salmon/**
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 salmon_index --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: salmon_quant
on:
push:
paths:
- software/salmon/quant/**
- .github/workflows/salmon_quant.yml
- tests/software/salmon/**
pull_request:
paths:
- software/salmon/quant/**
- .github/workflows/salmon_quant.yml
- tests/software/salmon/**
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 salmon_quant --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: samtools_mpileup
on:
push:
paths:
- software/samtools/mpileup/**
- .github/workflows/samtools_mpileup.yml
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/mpileup/**
- .github/workflows/samtools_mpileup.yml
- tests/software/samtools/**
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 samtools_mpileup --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: samtools_view
on:
push:
paths:
- software/samtools/view/**
- .github/workflows/samtools_view.yml
- tests/software/samtools/**
pull_request:
paths:
- software/samtools/view/**
- .github/workflows/samtools_view.yml
- tests/software/samtools/**
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 samtools_view --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: seacr_callpeak
on:
push:
paths:
- software/seacr/callpeak/**
- .github/workflows/seacr_callpeak.yml
- tests/software/seacr/**
pull_request:
paths:
- software/seacr/callpeak/**
- .github/workflows/seacr_callpeak.yml
- tests/software/seacr/**
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 seacr_callpeak --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: star_genomegenerate
on:
push:
paths:
- software/star/align/**
- .github/workflows/star_align.yml
- tests/software/star/**
pull_request:
paths:
- software/star/align/**
- .github/workflows/star_align.yml
- tests/software/star/**
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 star_align --symlink --wt 2

View file

@ -1,40 +0,0 @@
name: star_genomegenerate
on:
push:
paths:
- software/star/genomegenerate/**
- .github/workflows/star_genomegenerate.yml
- tests/software/star/**
pull_request:
paths:
- software/star/genomegenerate/**
- .github/workflows/star_genomegenerate.yml
- tests/software/star/**
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 star_genomegenerate --symlink --wt 2