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README.md

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preparation

Checkout the code, build or pull the image.

git clone

docker build -t huguesfontenelle/ubuntu-with-entrypoint .

or

docker pull huguesfontenelle/ubuntu-with-entrypoint

local

no ENTRYPOINT defined

nextflow  \
  run main.nf \
  -profile default_image \
  -work-dir "./work" \
  --outDir "./Results"

SUCCESS

ENTRYPOINT defined

nextflow  \
  -trace nextflow.cloud.google.pipelines \
  run main.nf \
  -profile entrypoint_image \
  -work-dir "./work" \
  --outDir "./Results"

SUCCESS

Google-genomics

Authenticate to GCP with your credentials and project ID.

export NXF_MODE=google
export GOOGLE_APPLICATION_CREDENTIALS="$HOME/.gcp/auth.json"
export GCP_PROJECT="my-gcp-project"
gcloud auth activate-service-account --key-file ${GOOGLE_APPLICATION_CREDENTIALS}
gcloud --quiet config set project ${GCP_PROJECT}
gcloud auth configure-docker

no ENTRYPOINT defined

nextflow  \
  -trace nextflow.cloud.google.pipelines \
  run main.nf \
  -profile gcp,default_image \
  -work-dir "gs://ngs-workdir/work" \
  --outDir "gs://ngs-workdir/Results"

SUCCESS

ENTRYPOINT defined

nextflow  \
  -trace nextflow.cloud.google.pipelines \
  run main.nf \
  -profile gcp,entrypoint_image \
  -work-dir "gs://ngs-workdir/work" \
  --outDir "gs://ngs-workdir/Results"

FAIL

Logs in .nextflow.log