From 6b38826af0447ac293f9f060e4c8a97fa8c42b0d Mon Sep 17 00:00:00 2001
From: Loraine Gueguen <loraine.gueguen@sb-roscoff.fr>
Date: Sun, 30 May 2021 19:36:46 +0200
Subject: [PATCH] Refactor run_wf (WIP)
---
constants_phaeo.py | 3 ---
gga_run_workflow_phaeo_jbrowse.py | 4 ----
2 files changed, 7 deletions(-)
diff --git a/constants_phaeo.py b/constants_phaeo.py
index 0457cc2..10cdb8c 100644
--- a/constants_phaeo.py
+++ b/constants_phaeo.py
@@ -40,9 +40,6 @@ WF_LOAD_GFF_JB_2_ORG_STEP_FEATURE_SYNC_ORG2 = "14"
WF_LOAD_GFF_JB_2_ORG_STEP_POPULATE_VIEWS = "15"
WF_LOAD_GFF_JB_2_ORG_STEP_INDEX = "16"
-WORKFLOW_BLAST = "blast"
-WORKFLOW_INTERPRO = "interpro"
-WORKFLOW_VALID_TYPES = [WF_LOAD_GFF_JB, WORKFLOW_BLAST, WORKFLOW_INTERPRO]
### Galaxy tools
diff --git a/gga_run_workflow_phaeo_jbrowse.py b/gga_run_workflow_phaeo_jbrowse.py
index 500f2a7..89a0718 100644
--- a/gga_run_workflow_phaeo_jbrowse.py
+++ b/gga_run_workflow_phaeo_jbrowse.py
@@ -347,10 +347,6 @@ if __name__ == "__main__":
type=str,
help="Where the stack containers will be located, defaults to working directory")
- parser.add_argument("--workflow", "-w",
- type=str,
- help="Worfklow to run. Available options: load_fasta_gff_jbrowse, blast, interpro")
-
args = parser.parse_args()
bioblend_logger = logging.getLogger("bioblend")
--
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