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mskcc / hermes

Data collection management and analysis of information
Apache License 2.0
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Implement ACCESS-Pipeline Operator #12

Open aef- opened 4 years ago

aef- commented 4 years ago
rhshah commented 4 years ago

@ionox0 can you help @aef- with examples of input YAML for each of this from the current ACCESS pipeline.

ionox0 commented 4 years ago

Ah so sorry for the delay, sure thing, I think the best way is to look at the /templates folder in the pipeline repo:

https://github.com/mskcc/ACCESS-Pipeline/tree/master/resources/templates

ionox0 commented 4 years ago

Sorry, that isn't the best way as it only lists the static resources / parameters.

Here are examples that also include dynamic run files (from the 10619_B production run):

ACCESS_pipeline.cwl /juno/work/access/production/runs/Project_10619_B/metadata/inputs_group_0.yaml call_cnv.cwl /juno/work/access/production/runs/Project_10619_B/copy_number_variants/inputs_cnv.yaml msi.cwl /juno/work/access/production/runs/Project_10619_B/microsatellite_instability/msi_inputs.yaml

manta.cwl and snps_and_indels.cwl /juno/work/access/production/runs/Project_10619_B/small_variants/vc_inputs.yaml

(it is possible to run a CWL workflow using just a subset of the inputs from the inputs file, which is why these two workflows use the same inputs file)