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Add tests for all samtools commands

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This commit is contained in:
drpatelh 2020-08-07 15:35:19 +01:00
parent 14480affba
commit 238f43789e
4 changed files with 120 additions and 0 deletions
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30
.github/workflows/samtools_idxstats.yml vendored Normal file
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@ -0,0 +1,30 @@
name: samtools_idxstats
on:
push:
paths:
- software/samtools/idxstats/**
- .github/workflows/samtools_idxstats.yml
- tests
pull_request:
paths:
- software/samtools/idxstats/**
- .github/workflows/samtools_idxstats.yml
- tests
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/
# Test the module
- run: nextflow run ./software/samtools/idxstats/test/ -profile docker

30
.github/workflows/samtools_index.yml vendored Normal file
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@ -0,0 +1,30 @@
name: samtools_index
on:
push:
paths:
- software/samtools/index/**
- .github/workflows/samtools_index.yml
- tests
pull_request:
paths:
- software/samtools/index/**
- .github/workflows/samtools_index.yml
- tests
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/
# Test the module
- run: nextflow run ./software/samtools/index/test/ -profile docker

30
.github/workflows/samtools_sort.yml vendored Normal file
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@ -0,0 +1,30 @@
name: samtools_sort
on:
push:
paths:
- software/samtools/sort/**
- .github/workflows/samtools_sort.yml
- tests
pull_request:
paths:
- software/samtools/sort/**
- .github/workflows/samtools_sort.yml
- tests
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/
# Test the module
- run: nextflow run ./software/samtools/sort/test/ -profile docker

30
.github/workflows/samtools_stats.yml vendored Normal file
View file

@ -0,0 +1,30 @@
name: samtools_stats
on:
push:
paths:
- software/samtools/stats/**
- .github/workflows/samtools_stats.yml
- tests
pull_request:
paths:
- software/samtools/stats/**
- .github/workflows/samtools_stats.yml
- tests
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/
# Test the module
- run: nextflow run ./software/samtools/stats/test/ -profile docker