fix: do not change fqscreen path with shared resources

they are no longer in shared resources dir

src/renee/gui.py

@@ -183,7 +183,7 @@ def launch_gui(sub_args, debug=True):
                     output_dir, os.environ.get("SINGULARITY_CACHEDIR", None)
                 ),
                 tmp_dir=get_tmp_dir(None, output_dir),
-                shared_resources=get_shared_resources_dir(None, output_dir),
+                shared_resources=get_shared_resources_dir(None),
                 star_2_pass_basic=False,
                 small_rna=False,
                 create_nidap_folder=False,

src/renee/setup.py

@@ -110,11 +110,6 @@ def setup(sub_args, ifiles, repo_path, output_path):
         ] = os.path.join(
             sub_args.shared_resources, "fastq_screen_db", "fastq_screen.conf"
         )
-        config["bin"]["rnaseq"]["tool_parameters"][
-            "FASTQ_SCREEN_CONFIG2"
-        ] = os.path.join(
-            sub_args.shared_resources, "fastq_screen_db", "fastq_screen_2.conf"
-        )
         config["bin"]["rnaseq"]["tool_parameters"]["KRAKENBACDB"] = os.path.join(
             sub_args.shared_resources, "20180907_standard_kraken2"
         )

src/renee/util.py

@@ -66,7 +66,7 @@ def get_tmp_dir(tmp_dir, outdir, hpc=get_hpcname()):
     return tmp_dir
 
 
-def get_shared_resources_dir(shared_dir, outdir, hpc=get_hpcname()):
+def get_shared_resources_dir(shared_dir, hpc=get_hpcname()):
     """Get default shared resources directory for biowulf and frce. Allow user override."""
     if not shared_dir:
         if hpc == "biowulf":

tests/test_run.py

@@ -9,7 +9,7 @@
     renee_base,
 )
 from renee.src.renee.cache import get_sif_cache_dir
-from renee.src.renee.run import run_in_context
+from renee.src.renee.run import run, run_in_context
 from renee.src.renee.util import get_hpcname
 
 
@@ -28,7 +28,7 @@ def test_dryrun():
                 sif_cache=get_sif_cache_dir(),
                 singularity_cache=os.environ["SINGULARITY_CACHEDIR"],
                 tmp_dir=tmp_dir,
-                shared_resources=None,
+                shared_resources=get_shared_resources_dir(None),
                 star_2_pass_basic=False,
                 small_rna=False,
                 create_nidap_folder=False,