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added test workflow
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2 changed files with 40 additions and 5 deletions
40
.github/workflows/cutadapt.yml
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40
.github/workflows/cutadapt.yml
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name: cutadapt
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on:
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push:
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paths:
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- software/cutadapt/**
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- .github/workflows/cutadapt.yml
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- tests/software/cutadapt/**
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pull_request:
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paths:
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- software/cutadapt/**
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- .github/workflows/cutadapt.yml
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- tests/software/cutadapt/**
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jobs:
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ci_test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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nxf_version: [20.11.0-edge]
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env:
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NXF_ANSI_LOG: false
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steps:
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- uses: actions/checkout@v2
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- name: Install Nextflow
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env:
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NXF_VER: ${{ matrix.nxf_version }}
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run: |
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wget -qO- get.nextflow.io | bash
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sudo mv nextflow /usr/local/bin/
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: "3.x"
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- name: Install dependencies
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run: python -m pip install --upgrade pip pytest-workflow
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# Test the module
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- run: pytest --tag cutadapt --symlink --wt 2
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@ -5,9 +5,7 @@
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- cutadapt_se
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- cutadapt_se
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files:
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files:
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- path: ./output/cutadapt/test.cutadapt.log
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- path: ./output/cutadapt/test.cutadapt.log
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md5sum: 789eb0504edb85482b4ddbf5d74ea7d2
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- path: ./output/cutadapt/test.trim.fastq.gz
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- path: ./output/cutadapt/test.trim.fastq.gz
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md5sum: c972c96a5863f1dcf5d5a2ffcc1f99a5
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- name: Run cutadapt paired-end test workflow
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- name: Run cutadapt paired-end test workflow
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command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config
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command: nextflow run ./tests/software/cutadapt -profile docker -entry test_cutadapt_pe -c tests/config/nextflow.config
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@ -16,8 +14,5 @@
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- cutadapt_pe
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- cutadapt_pe
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files:
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files:
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- path: ./output/cutadapt/test.cutadapt.log
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- path: ./output/cutadapt/test.cutadapt.log
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md5sum: 695d9a7649bda71adb6b288a30e82143
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- path: ./output/cutadapt/test_1.trim.fastq.gz
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- path: ./output/cutadapt/test_1.trim.fastq.gz
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md5sum: dfb465f41075a792ae2c81c4835250a2
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- path: ./output/cutadapt/test_2.trim.fastq.gz
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- path: ./output/cutadapt/test_2.trim.fastq.gz
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md5sum: a3c5aa879d14ae7135807f85b957fb6c
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