publish.conseq

rule publish_cngene_log2:
    inputs:
        cngene_log2={"type": "cngene_log2"},
        release_taiga_id={"type": "release_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "release_cngene_log2_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Updated cngene log2 data for release'  'PortalOmicsCNGeneLog2' {{inputs.cngene_log2.filename}} 'csv_matrix'"


rule publish_filtered_portal_compounds:
    inputs:
        filtered_portal_compounds={"type": "filtered_portal_compounds"},
        release_taiga_id={"type": "release_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "release_filtered_portal_compounds_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Filtered portal compounds data for release' 'PortalCompounds' {{inputs.filtered_portal_compounds.filename}} 'csv_table'"


rule publish_driver_events:
    inputs:
        driver_events_data={"type": "predictability_driver_events"},
        predictability_taiga_id={"type": "predictability_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "predictability_driver_events_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.predictability_taiga_id.dataset_id}} 'Generated driver events data for predictability'  'PredictabilityDriverEventsTransformed' {{inputs.driver_events_data.filename}} 'csv_matrix'"


rule publish_genetic_derangement:
    inputs:
        genetic_derangement_data={"type": "predictability_genetic_derangement"},
        predictability_taiga_id={"type": "predictability_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "predictability_genetic_derangement_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.predictability_taiga_id.dataset_id}} 'Generated genetic derangement data for predictability'  'PredictabilityGeneticDerangementTransformed' {{inputs.genetic_derangement_data.filename}} 'csv_matrix'"


rule publish_fusion:
    inputs:
        fusion_data={"type": "predictability_fusion"},
        predictability_taiga_id={"type": "predictability_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "predictability_fusion_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.predictability_taiga_id.dataset_id}} 'Generated fusion data for predictability'  'PredictabilityFusionTransformed' {{inputs.fusion_data.filename}} 'csv_matrix'"


rule publish_lineage:
    inputs:
        lineage_data={"type": "predictability_lineage"},
        predictability_taiga_id={"type": "predictability_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "predictability_lineage_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.predictability_taiga_id.dataset_id}} 'Generated lineage data for predictability'  'PredictabilityLineageTransformed' {{inputs.lineage_data.filename}} 'csv_matrix'"


rule publish_crispr_confounders:
    inputs:
        crispr_confounders_data={"type": "predictability_crispr_confounders"},
        predictability_taiga_id={"type": "predictability_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "predictability_crispr_confounders_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.predictability_taiga_id.dataset_id}} 'Generated CRISPR confounders data for predictability'  'PredictabilityCRISPRConfoundersTransformed' {{inputs.crispr_confounders_data.filename}} 'csv_matrix'"

rule publish_subtype_tree:
    inputs:
        subtype_tree={"type": "subtype_tree"},
        release_taiga_id={"type": "release_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "release_subtype_tree_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Created SubtypeTree for release'  'SubtypeTree' {{inputs.subtype_tree.filename}} 'csv_table'"

rule publish_context_matrix:
    inputs:
        context_matrix={"type": "context_matrix"},
        release_taiga_id={"type": "release_taiga_id"},
        update_taiga_script=fileref('upload_to_taiga.py')
    outputs:{"type": "release_context_matrix_published"}

    run "python3 {{inputs.update_taiga_script.filename}} {{inputs.release_taiga_id.dataset_id}} 'Created ContextMatrix for release'  'SubtypeMatrix' {{inputs.context_matrix.filename}} 'csv_matrix'"