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Description
Need to figure out how we can handle launch method for pipelines with different CEs, and different workdirs/etc accordingly.
For example:
launch:
- name: 'nf-core-rnaseq-url-launch' ## Remote launch
pipeline: 'https://github.com/nf-core/rnaseq'
profile: 'test'
revision: '3.12.0'
workspace: 'tw_cli_e2e_test/showcase'
workspace-secrets: 'SENTIEON_LICENSE_BASE64'
compute-envs:
- name: 'seqera_aws_ireland_fusionv2_nvme'
work-dir: 's3://seqeralabs-showcase'
params:
outdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'
config: './pipelines/nextflow.config'
pre-run: './pipelines/pre_run.txt'
- name: 'seqera_gcp_finland'
work-dir: 'gs://seqeralabs-showcase-eu-north-1'
params-file: './pipelines/nf_core_rnaseq_params.yml'
- name: 'nf-core-rnaseq-launchpad-launch' ## Launchpad launch
pipeline: 'nf-core-rnaseq'
workspace: 'tw_cli_e2e_test/showcase'
compute-envs:
- name: 'seqera_aws_ireland_fusionv2_nvme'
work-dir: 's3://seqeralabs-showcase'
params:
outdir: 's3://seqeralabs-showcase/nf-core-rnaseq/results'
config: './pipelines/nextflow.config'
pre-run: './pipelines/pre_run.txt'
- name: 'seqera_gcp_finland'
work-dir: 'gs://seqeralabs-showcase-eu-north-1'
params-file: './pipelines/nf_core_rnaseq_params.yml'
Some things to think about:
- How do we handle running the launch method on every
pipelinekey with different options forcompute-envs,params-file... - We can parse the
work-dirfrom CE if we output the JSON using the list method instead of explicitly specifying it here everytime - If
urlis specified forpipeline, certain options will be required by default but if only the launchpad name is specified, than many options will be pre-configred. Can these be overriden via CLI? Need to test.
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