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Merge pull request #1 from papaemmelab/add-test
✅ Add ci with nf-test
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Original file line number | Diff line number | Diff line change |
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@@ -5,6 +5,7 @@ capsule | |
framework | ||
pipeline_* | ||
.nextflow* | ||
.nf-test* | ||
tmp | ||
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# Tests | ||
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FROM nextflow/nextflow | ||
FROM papaemmelab/docker-hmftools:v1.0.0 | ||
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# Install dependencies | ||
RUN yum install -y tar | ||
RUN apt-get update && apt-get install -y tar curl python3 | ||
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# Install https://github.com/askimed/nf-test | ||
RUN mkdir -p /opt/bin && \ | ||
cd /opt/bin && \ | ||
curl -fsSL https://code.askimed.com/install/nf-test | bash && \ | ||
export PATH=/opt/bin:$PATH && \ | ||
nf-test version | ||
# Install Google Cloud SDK | ||
RUN curl -sSL https://sdk.cloud.google.com | bash | ||
ENV PATH $PATH:/root/google-cloud-sdk/bin | ||
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# Set version as an environment variable | ||
ENV GENOME_VERSION=37 | ||
ENV HMFTOOLS_VERSION=5.33 | ||
ENV HMFTOOLS_VERSION_UNDERSCORE 5_33 | ||
ENV REF_DIR=hmf_dna_pipeline_resources.${GENOME_VERSION}_v${HMFTOOLS_VERSION} | ||
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# Download the file using gsutil | ||
RUN \ | ||
mkdir -p /data && \ | ||
gsutil cp gs://hmf-public/HMFtools-Resources/dna_pipeline/v${HMFTOOLS_VERSION_UNDERSCORE}/${GENOME_VERSION}/${REF_DIR}.tar.gz /data/ && \ | ||
tar -xzf /data/${REF_DIR}.tar.gz -C /data && \ | ||
rm /data/${REF_DIR}.tar.gz | ||
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COPY . /app | ||
WORKDIR /app | ||
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ENTRYPOINT ["nextflow", "-version"] | ||
ENTRYPOINT ["bash", "-c"] |
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config { | ||
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testsDir "tests" | ||
workDir ".nf-test" | ||
configFile "tests/nextflow.config" | ||
profile "cloud" | ||
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} |
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