gga_run_workflow_jbrowse workflow parameters names matching constants_phaeo.py

constants_phaeo.py

@@ -8,8 +8,7 @@ import constants
 
 WORKFLOWS_PATH = "workflows_phaeoexplorer/"
 
-# Workflow to load the genome and annotations into chado, create/update organisms in a jbrowse instance
-WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v6.ga"
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v7.ga"
 WF_LOAD_GFF_JB_1_ORG_INPUT_GENOME = "0"
 WF_LOAD_GFF_JB_1_ORG_INPUT_GFF = "1"
 WF_LOAD_GFF_JB_1_ORG_INPUT_PROTEINS = "2"
@@ -17,28 +16,37 @@ WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_FASTA = "3"
 WF_LOAD_GFF_JB_1_ORG_STEP_JBROWSE = "4"
 WF_LOAD_GFF_JB_1_ORG_STEP_LOAD_GFF = "5"
 WF_LOAD_GFF_JB_1_ORG_STEP_JB_TO_CONTAINER = "6"
-WF_LOAD_GFF_JB_1_ORG_STEP_FEATURE_SYNC = "7"
-WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "8"
-WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "9"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_FEATURE = "7"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_ORG = "8"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_GENOME_ANALYSIS = "9"
+WF_LOAD_GFF_JB_1_ORG_STEP_SYNC_OGS_ANALYSIS = "10"
+WF_LOAD_GFF_JB_1_ORG_STEP_POPULATE_VIEWS = "11"
+WF_LOAD_GFF_JB_1_ORG_STEP_INDEX = "12"
 
-WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v6.ga"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "0"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "1"
-WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "2"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "3"
-WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "4"
+WF_LOAD_GFF_JB_2_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_2org_v7.ga"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG1 = "4"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG1 = "2"
+WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG1 = "0"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GENOME_ORG2 = "1"
+WF_LOAD_GFF_JB_2_ORG_INPUT_GFF_ORG2 = "3"
 WF_LOAD_GFF_JB_2_ORG_INPUT_PROTEINS_ORG2 = "5"
-WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1 = "6"
-WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "7"
-WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2 = "8"
+WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG1 = "7"
+WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG1 = "8"
+WF_LOAD_GFF_JB_2_ORG_STEP_JBROWSE_ORG2 = "6"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG1 = "9"
 WF_LOAD_GFF_JB_2_ORG_STEP_JB_TO_CONTAINER = "10"
 WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG1 = "11"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_FASTA_ORG2 = "12"
 WF_LOAD_GFF_JB_2_ORG_STEP_LOAD_GFF_ORG2 = "13"
 WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_FEATURE_ORG2 = "14"
-WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "15"
-WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "16"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG1 = "15"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_ORG2 = "16"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG1 = "17"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG1 = "18"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_GENOME_ANALYSIS_ORG2 = "19"
+WF_LOAD_GFF_JB_2_ORG_STEP_SYNC_OGS_ANALYSIS_ORG2 = "20"
+WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "21"
+WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "22"
 
 # Workflow to load blastp, blastx and interproscan into chado and tripal
 WF_BLAST_INTERPRO_1_ORG_FILE = "Galaxy-Workflow-load_blast_interproscan_results_1org_v2.ga"

gga_run_workflow_phaeo_jbrowse.py

@@ -257,7 +257,6 @@ class RunWorkflowJbrowse(gga_run_workflow_phaeo.RunWorkflow):
         self.transcripts_hda_id = transcripts_hda_id
         self.proteins_hda_id = proteins_hda_id
 
-
 def prepare_history_and_get_wf_param(sp_dict_list, main_dir, config):
 
     all_org_wf_param_dict = {}