SC Lab: Content Yaml cleanup

[billtell]

There has been a lot of reagent and duplicate protocols commented out in the content.yml file since the reconfiguration of the SC wfc. This branch is for fully removing these protocols from the content yml to make the file more readable and accurate to what is now being used.

[billtell]

• Protocols
• model: protocol data: $LAB7DATA/content/protocols/sc_3_prime_qubit_and_agilent_2_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_qubit_and_agilent_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_adaptor_ligation_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_cdna_amp_cleanup_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_cdna_amplification_reaction_reagents_protocol.yml
  • model: protocol
    data: $LAB7DATA/content/protocols/sc_3_prime_dual_spri_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_dyna_beads_cleanup_mix_reagents_protocol.yml
  • model: protocol
    data: $LAB7DATA/content/protocols/sc_3_prime_elution_solution_i_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_fragmentation_end_repair_and_a-tailing_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_gem_generation_and_barcoding_reagents_lot_inventory_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_post_ligation_clean_up_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_post_pcr_clean_up_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_sample_feature_index_pcr_mix_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_sample_index_pcr_mix_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_existing_cdna.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_3_prime_existing_cdna_aliquot.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_agilent_hs_2_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_agilent_hs_3_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_enrichment_library_barcode_2_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_enrichment_library_barcode_3_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_enrichment_library_barcode_4_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_adaptor_ligation_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_adaptor_ligation_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_adaptor_ligation_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_adaptor_ligation_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_adaptor_ligation_reagents_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_cdna_amp_cleanup_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_cdna_amplification_reaction_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_dual_spri_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_dual_spri_reagents_3_protocol.yml
  • model: protocol
    data: $LAB7DATA/content/protocols/sc_5_prime_dyna_beads_cleanup_mix_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_elution_solution_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_existing_cdna.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_existing_cdna_aliquot.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_fragmentation_end_repair_and_a-tailing_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_fragmentation_end_repair_and_a-tailing_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_fragmentation_end_repair_and_a-tailing_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_fragmentation_end_repair_and_a-tailing_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_fragmentation_end_repair_and_a-tailing_reagents_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_gem_generation_and_barcoding_reagents_lot_inventory_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_enrichment_spri_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_enrichment_1_spri_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_enrichment_dual_spri_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_enrichment_2_dual_spri_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_ligation_clean_up_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_ligation_clean_up_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_ligation_clean_up_reagents_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_pcr_clean_up_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_pcr_clean_up_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_pcr_clean_up_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_post_pcr_clean_up_reagents_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_5_prime_qubit_and_agilent_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_qubit_and_agilent_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_qubit_and_agilent_4_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_concentration_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_concentration_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_feature_index_pcr_mix_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_index_pcr_mix_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_index_pcr_mix_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_index_pcr_mix_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_index_pcr_mix_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_sample_index_pcr_mix_reagents_3_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_1_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_1_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_2_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_2_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_5_prime_target_enrichment_2_reagents_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_adaptor_ligation_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_agilent_hs_2_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_atac_library_cleanup_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_atac_library_reagents_lot_inventory_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_cdna_amp_cleanup_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_cdna_amplification_reaction_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_dual_spri_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_existing_cdna.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_multiome_existing_cdna_aliquot.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_fragmentation_end_repair_and_a-tailing_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_pre-amp_reagents_lot_inventory_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_post_ligation_clean_up_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_post_pcr_clean_up_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_pre-amp_cleanup_reagents_protocol.yml
• model: protocol
  data: $LAB7DATA/content/protocols/sc_multiome_sample_index_pcr_mix_reagents_protocol.yml
• model: protocol
  data:$LAB7DATA/content/protocols/sc_multiome_transposition_and_gem_generation_and_barcoding_reagents_lot_inventory_protocol.yml
• model: protocol data: $LAB7DATA/content/protocols/sc_multiome_post_gem_incubation_cleanup_reagents_lot_inventory_protocol.yml

[billtell]

Workflows

• model: workflow
  data: $LAB7DATA/content/workflows/sc_3_v_3.1_gex_only_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_3_v_3.1_gex_only_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_3_v_3.1_gex_with_feature_cellplex-crispr_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_3_v_3.1_gex_with_feature_totalseq_a-b_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_3P_existing_cdna.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5P_existing_cdna.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_only_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gexonly-_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_1_enrichment_tcr-bcr_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_1_enrichment_tcr-bcr_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_1_enrichment_tcr-bcr_feature_totalseqc_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_1_enrichment_tcr-bcr_feature_totalseqc_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_2_enrichments_tcr-bcr_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_2_enrichments_tcr-bcr_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_2_enrichments_tcr-bcr_feature_totalseqc_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_2_enrichments_tcr-bcr_feature_totalseqc_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_feature_totalseqc_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_5_v_2_gex_with_feature_totalseqc_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_multiome_existing_cdna.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_multiome_3_v_3.1_and_atac_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_multiome_3_v_3.1_and_atac_existing_cdna_workflow.yml

• model: workflow data: $LAB7DATA/content/workflows/sc_labkey_checkin_workflow.yml

[billtell]

Workflow Chain

• model: workflow_chain data: $LAB7DATA/content/chains/sc_wf_chain.yml