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Launch functionality with multiple CEs #14

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ejseqera opened this issue Jun 20, 2023 · 0 comments
Open

Launch functionality with multiple CEs #14

ejseqera opened this issue Jun 20, 2023 · 0 comments
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enhancement New feature or request

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@ejseqera
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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.
@ejseqera ejseqera added the enhancement New feature or request label Jun 23, 2023
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