Update Python wf

bioexcel · Jan 13, 2025 · 126a8da · 126a8da
1 parent 2011148
commit 126a8da
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/biobb_wf_amber_md_setup/python/workflow.env.yml b/biobb_wf_amber_md_setup/python/workflow.env.yml
@@ -3,7 +3,7 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - biobb_structure_utils>=4.2.0
-  - biobb_chemistry>=4.2.0
-  - biobb_amber>=4.2.0
-  - biobb_analysis>=4.2.0
+  - biobb_structure_utils>=5.0.0
+  - biobb_chemistry>=5.0.3
+  - biobb_amber>=5.0.2
+  - biobb_analysis>=5.0.1
diff --git a/biobb_wf_amber_md_setup/python/workflow.yml b/biobb_wf_amber_md_setup/python/workflow.yml
@@ -5,7 +5,7 @@ run_md: true
 step00_reduce_remove_hydrogens:
   tool: reduce_remove_hydrogens
   paths:
-    input_path: /path/to/inputs/structure.pdb
+    input_path: file:structure.pdb
     output_path: structure.noH.pdb
 
 step0_extract_molecule:
@@ -18,7 +18,7 @@ step000_cat_pdb:
   tool: cat_pdb
   paths:
     input_structure1: dependency/step0_extract_molecule/output_molecule_path
-    input_structure2: /path/to/inputs/ions.pdb
+    input_structure2: file:ions.pdb
     output_structure_path: protein.ions.pdb
 
 step1_pdb4amber_run: