Refactor run_wf (WIP)

phaoexplorer_constants.py → phaeoexplorer_constants.py

@@ -6,11 +6,23 @@ import constants
 ### Workflows
 
 WORKFLOWS_PATH = "workflows_phaeoexplorer/"
-WORKFLOW_LOAD_FASTA_GFF_JBROWSE = "load_fasta_gff_jbrowse"
-WORKFLOW_LOAD_FASTA_GFF_JBROWSE_FILE_1_ORG = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v4.ga"
+WF_LOAD_GFF_JB = "load_fasta_gff_jbrowse"
+
+WF_LOAD_GFF_JB_1_ORG_FILE = "Galaxy-Workflow-chado_load_tripal_synchronize_jbrowse_1org_v4.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"
+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"
+
 WORKFLOW_BLAST = "blast"
 WORKFLOW_INTERPRO = "interpro"
-WORKFLOW_VALID_TYPES = [WORKFLOW_LOAD_FASTA_GFF_JBROWSE, WORKFLOW_BLAST, WORKFLOW_INTERPRO]
+WORKFLOW_VALID_TYPES = [WF_LOAD_GFF_JB, WORKFLOW_BLAST, WORKFLOW_INTERPRO]
 
 ### Galaxy tools