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
pipeline key with different options for compute-envs, params-file...
- We can parse the
work-dir from CE if we output the JSON using the list method instead of explicitly specifying it here everytime
- If
url is specified for pipeline, 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.
Need to figure out how we can handle launch method for pipelines with different CEs, and different workdirs/etc accordingly.
For example:
Some things to think about:
pipelinekey with different options forcompute-envs,params-file...work-dirfrom CE if we output the JSON using the list method instead of explicitly specifying it here everytimeurlis 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.