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.gitlab-ci.yml
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.gitlab-ci.yml
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# Build the docker image and publish it to gitlabs repository
image:
name: registry.hub.docker.com/nextflow/nextflow:22.04.5
services:
# - docker:20.10.14-dind
- name: registry.hub.docker.com/library/docker:20.10.14-dind
command: ["--tls=false"]
alias: docker
variables:
DOCKER_HOST: tcp://docker:2375/
# nextflow-mock:
# stage: deploy
# environment:
# name: mock
# url: $PUBLISH_URL
# script:
# - echo $ARTIFACT_REPOSITORY
# - echo $ARTIFACT_REPOSITORY_TOKEN
# - echo $CI_JOD_IMAGE
# - echo $CI_STAHL_REGISTRY_TOKEN
# - echo $CI_STORE_TOKEN
# - echo $CI_XLSX2OWL_IMAGE
# - echo $DSMS_PASSWORD
# - echo $DSMS_USER
# - echo $INPUT_FILE
# - echo $PUBLISH_REPOSITORY_KEY
# - echo $PUBLISH_REPOSITORY
# - echo $PUBLISH_URL
# - echo $QUITSTORE_TOKEN
# - echo $QUITSTORE_USER
# - nextflow run . --xlsxUrl=$INPUT_FILE
nextflow:
# stage: deploy
stage: build
artifacts:
when: always
paths:
- $ARTIFACT_FOLDER/*
- pipeline_trace.txt
- .nextflow.log
rules:
- if: $CI_COMMIT_BRANCH != "main"
allow_failure:
exit_codes: # User defined exit code
- 22
script:
- echo $ARTIFACT_REPOSITORY
- echo $ARTIFACT_REPOSITORY_TOKEN
- echo $CI_JOD_IMAGE
- echo $CI_STAHL_REGISTRY_TOKEN
- echo $CI_STORE_TOKEN
- echo $CI_XLSX2OWL_IMAGE
- echo $DSMS_PASSWORD
- echo $DSMS_USER
- echo $INPUT_FILE
- echo $PUBLISH_REPOSITORY_KEY
- echo $PUBLISH_REPOSITORY_VERSIONING_KEY
- echo $PUBLISH_REPOSITORY
- echo $PUBLISH_URL
- echo $QUITSTORE_TOKEN
- echo $QUITSTORE_USER
- echo $KNOWN_HOSTS
- nextflow run . --xlsxUrl=$INPUT_FILE --publish=true
- _status=$?
- if [ ! $_status ]; then exit $_status; fi;
- if [ ! "$(grep -e 'v2d.*\s0' pipeline_trace.txt)" ]; then exit 22; fi;
- cat pipeline_trace.txt
nextflow-main:
stage: deploy
artifacts:
when: always
paths:
- $ARTIFACT_FOLDER/*
- pipeline_trace.txt
- .nextflow.log
rules:
- if: $CI_COMMIT_BRANCH == "main"
environment:
name: main
url: $PUBLISH_URL
allow_failure:
exit_codes: # User defined exit code
- 22
script:
- echo $ARTIFACT_REPOSITORY
- echo $ARTIFACT_REPOSITORY_TOKEN
- echo $CI_JOD_IMAGE
- echo $CI_STAHL_REGISTRY_TOKEN
- echo $CI_STORE_TOKEN
- echo $CI_XLSX2OWL_IMAGE
- echo $DSMS_PASSWORD
- echo $DSMS_USER
- echo $INPUT_FILE
- echo $PUBLISH_REPOSITORY_KEY
- echo $PUBLISH_REPOSITORY_VERSIONING_KEY
- echo $PUBLISH_REPOSITORY
- echo $PUBLISH_URL
- echo $QUITSTORE_TOKEN
- echo $QUITSTORE_USER
- nextflow run . --xlsxUrl=$INPUT_FILE --publish=true
- _status=$?
- if [ ! $_status ]; then exit $_status; fi;
- if [ ! "$(grep -e 'v2d.*\s0' pipeline_trace.txt)" ]; then exit 22; fi;
- cat pipeline_trace.txt