briandoconnor

{
   "missing_items" : {
      "tumor_rna_seq_cgl_workflow_3_0_x" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],
      "normal_rna_seq_cgl_workflow_3_0_x" : [],
      "normal_sequence" : [],
      "tumor_alignment_qc_report" : [
         "3398874d-0f93-5737-bf19-32a36c9191dc"
      ],

briandoconnor

/home/ubuntu/envs/env-ga4gh-dream/bin/cwltool 1.0.20170217172322
Resolved 'main-NA12878-platinum-chr20.cwl' to 'file:///home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl'
[job alignment_to_rec] Output of job will be cached in /home/ubuntu/ga4gh_dream_testing/bcbio/NA12878-platinum-chr20-workflow/cache/68761c321fc424b99b4ba5719b935567
['docker', 'pull', 'quay.io/bcbio/bcbio-base']
Using default tag: latest
latest: Pulling from bcbio/bcbio-base
75c416ea735c: Pulling fs layer
c6ff40b6d658: Pulling fs layer
a7050fc1f338: Pulling fs layer
f0ffb5cf6ba9: Pulling fs layer

briandoconnor

/home/ubuntu/envs/env-ga4gh-dream/bin/cwltool 1.0.20170217172322
Resolved 'main-NA12878-platinum-chr20.cwl' to 'file:///home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl'
[job prep_samples_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/a5cb782c5a69dcd3836c6f6aaad47e4e
['docker', 'pull', 'quay.io/bcbio/bcbio-base']
Using default tag: latest
latest: Pulling from bcbio/bcbio-base
75c416ea735c: Pulling fs layer
c6ff40b6d658: Pulling fs layer
a7050fc1f338: Pulling fs layer
f0ffb5cf6ba9: Pulling fs layer

briandoconnor

/home/ubuntu/envs/env-ga4gh-dream-bcbio/bin/cwltool 1.0.20170413194156
Resolved 'main-NA12878-platinum-chr20.cwl' to 'file:///home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/main-NA12878-platinum-chr20.cwl'
[job alignment_to_rec] Output of job will be cached in /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/fff9469d1a8ae685c1e99c2596513fb1
[job alignment_to_rec] /home/ubuntu/ga4gh-challenge-test/bcbio/NA12878-platinum-chr20-workflow/cache/fff9469d1a8ae685c1e99c2596513fb1$ docker \
    run \
    -i \
    --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/bwa-wf.tar.gz:/var/lib/cwl/stgea1545d6-7249-4453-bce3-d36d6bef00ae/bwa-wf.tar.gz:ro \
    --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/collections/hg38/seq/hg38.fa:/var/lib/cwl/stg807544db-f43d-4803-b59f-c63f2a957887/hg38.fa:ro \
    --volume=/home/ubuntu/ga4gh-challenge-test/bcbio/biodata/giab/na12878/NA12878-platinum-chr20.bam:/var/lib/cwl/stg850be498-493c-4a0b-ab2f-63b5

briandoconnor

openapi: 3.0.0
servers:
  - url: /api/v1
info:
  title: GA4GH Workflow Execution API
  description: >-
    Proposed API for GA4GH workflow execution. A workflow is defined with a
    given format (currently CWL or WDL) and can encompass a single tool
    execution or a complex DAG of individual tool calls. The parameterization of
    the workflow called will follow the schema proposed in this group as a

briandoconnor

- See issue [#29](https://github.com/ga4gh/TASC/issues/29)
- See issue [#325](https://github.com/ga4gh/data-repository-service-schemas/issues/325)
- Question 1: are we settled on using the GitHub pagination style?
  
  Query params:
  - optional:
    - per_page
    - page 
  Links: header
  - required:

briandoconnor

{
  "objectids": [
    "s291293",
    "lksdflkjs"
  ]
}

briandoconnor

# POST for access from /bulk/objects/access method

{
  "object_access_ids": [
    { "object_id": "",
      "access_id": ""
    }
  ]
}