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Merge pull request #128 from JoseEspinosa/bowtie2_viralrecon

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Bowtie2 viralrecon 2
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Harshil Patel 2021-02-01 09:56:11 +00:00 committed by GitHub
commit c74d8a1711
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3 changed files with 86 additions and 4 deletions
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42
.github/workflows/bowtie2_align.yml vendored Normal file
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@ -0,0 +1,42 @@
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

40
.github/workflows/bowtie2_build.yml vendored Normal file
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@ -0,0 +1,40 @@
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

8
tests/software/bowtie2/test.yml
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@ -47,17 +47,17 @@
- bowtie2_align - bowtie2_align
files: files:
- path: output/bowtie2/bowtie2/NC_010473.1.bt2 - path: output/bowtie2/bowtie2/NC_010473.1.bt2
md5sum: 90f0b7aa5bbaeaaa999839ac13ad203c md5sum: 4db22d92e72111a5fbf609b3d9a43015
- path: output/bowtie2/bowtie2/NC_010473.2.bt2 - path: output/bowtie2/bowtie2/NC_010473.2.bt2
md5sum: bfd10c5319c6a0dbc540fd789254a5dd md5sum: f4429ec74ee0064732c4bb26718a3eb1
- path: output/bowtie2/bowtie2/NC_010473.3.bt2 - path: output/bowtie2/bowtie2/NC_010473.3.bt2
md5sum: cd201e81724f3099131aec16ef2cc53b md5sum: cd201e81724f3099131aec16ef2cc53b
- path: output/bowtie2/bowtie2/NC_010473.4.bt2 - path: output/bowtie2/bowtie2/NC_010473.4.bt2
md5sum: bbb9d6d21ad765d135f95290204e8433 md5sum: bbb9d6d21ad765d135f95290204e8433
- path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2 - path: output/bowtie2/bowtie2/NC_010473.rev.1.bt2
md5sum: 44f719c2fe42e1f35d54e798775846d1 md5sum: 4ccfee8857c3b1c69857e5ecdef597aa
- path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2 - path: output/bowtie2/bowtie2/NC_010473.rev.2.bt2
md5sum: f3c398bba5158f4039334a932d79c051 md5sum: 5e8fb4af677eb3a57a40e76dc3f6db72
- path: output/bowtie2/test.bowtie2.log - path: output/bowtie2/test.bowtie2.log
md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5 md5sum: 9f9eb40b5f57e0f2d5c874f2c1b5cfd5
- path: output/bowtie2/test.bam - path: output/bowtie2/test.bam