From a42920d63ca707f35dc537e0a3608b4e350f17dd Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Wed, 14 Apr 2021 11:58:07 +0200
Subject: [PATCH] parameters fix
---
run_workflow_phaeoexplorer.py | 2 +-
speciesData.py | 1 +
2 files changed, 2 insertions(+), 1 deletion(-)
diff --git a/run_workflow_phaeoexplorer.py b/run_workflow_phaeoexplorer.py
index e97f1fe..fe77cef 100755
--- a/run_workflow_phaeoexplorer.py
+++ b/run_workflow_phaeoexplorer.py
@@ -492,7 +492,7 @@ class RunWorkflow(speciesData.SpeciesData):
# In case of the Jbrowse workflow, we unfortunately have to manually edit the parameters instead of setting them
# as runtime values, using runtime parameters makes the tool throw an internal critical error ("replace not found" error)
# Scratchgmod test: need "http" (or "https"), the hostname (+ port)
- if not self.config["menu_url"]:
+ if "menu_url" not in self.config.keys():
jbrowse_menu_url = "https://{hostname}/sp/{genus_sp}/feature/{Genus}/{species}/{id}".format(hostname=self.config["hostname"], genus_sp=self.genus_species, Genus=self.genus_uppercase, species=self.species, id="{id}")
else:
jbrowse_menu_url = self.config["menu_url"]
diff --git a/speciesData.py b/speciesData.py
index cf9da39..a2fcbdb 100755
--- a/speciesData.py
+++ b/speciesData.py
@@ -80,6 +80,7 @@ class SpeciesData:
self.datasets = dict()
self.config = None # Custom config used to set environment variables inside containers
self.species_folder_name = "_".join(utilities.filter_empty_not_empty_items([self.genus_lowercase.lower(), self.species.lower(), self.strain.lower(), self.sex.lower()])["not_empty"])
+ self.species_folder_name = self.species_folder_name .replace("-", "_")
self.existing_folders_cache = {}
self.bam_metadata_cache = {}
--
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