fix formats

Author: ndonyapour

examples/docking/docking_stability.wic

@@ -31,16 +31,16 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup_vac_min.yml):
+          (1, setup_vac_min.wic):
             wic:
               steps:
-                (3, solv_ion.yml):
+                (3, solv_ion.wic):
                   wic:
                     steps:
                       (4, genion):
                         in:
                           output_top_zip_path: !& genion_complex.zip
-          (2, basic.yml):
+          (2, basic.wic):
             in:
               top_zip_path: !* genion_complex.zip
             wic:
@@ -54,7 +54,7 @@ wic:
                       (3, mdrun):
                         in:
                           output_crd_path: !& prod_complex.gro
-                      (4, cwl_watcher_analysis.yml):
+                      (4, cwl_watcher_analysis.wic):
                         wic:
                           implementation: complex
           (3, analysis.wic):
@@ -63,6 +63,6 @@ wic:
                 (1, analysis_realtime.wic):
                   wic:
                     backend: complex
-                (2, analysis_final.yml):
+                (2, analysis_final.wic):
                   wic:
                     backend: complex

examples/docking/gen_topol_params.wic

@@ -79,7 +79,8 @@ steps:
       input_structure1: input_receptor_xyz_path
       input_structure2: !* pose_ligand.xyz
       input_top_zip_path: !* complex_vac.zip
-      output_structure_path: !& complex_vac.pdb
+    out:
+    - output_structure_path: !& complex_vac.pdb
 
 wic:
   graphviz:

examples/docking/vs_demo_4.wic

@@ -206,14 +206,19 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.wic):
+          (1, setup_vac_min.wic):
             wic:
               steps:
-                (4, genion):
-                  out:
-                  - output_top_zip_path: !& genion_complex.zip
+                (3, solv_ion.wic):
+                  wic:
+                    steps:
+                      (4, genion):
+                        out:
+                            - output_top_zip_path: !& genion_complex.zip
           (2, basic.wic):
-            wic:
+            in: 
+              top_zip_path: !* genion_complex.zip
+            wic: 
               steps:
                 (3, prod.wic):
                   wic:

examples/gromacs/basic.wic

@@ -19,16 +19,16 @@ steps:
 # (i.e. immediately before molecular dynamics) so we can extract &min.tpr
 # to this level and use the following syntax to pass it to only one call site.
 # (Moreover, the former will create multiple definitions of &min.tpr, which is not allowed.)
-  - min.yml:
-      in:
-        top_zip_path: top_zip_path
-  - equil.yml:
-  - prod.yml:
-      in:
-        nsteps: nsteps
-        dt: dt
-        ref-t: ref-t
-        ref-p: ref-p
+  min.wic:
+    in:
+      top_zip_path: top_zip_path
+  equil.wic:
+  prod.wic:
+    in:
+      nsteps: nsteps
+      dt: dt
+      ref-t: ref-t
+      ref-p: ref-p
 
 # Pass the CWL `in` tag as a parameter through BOTH of the yml DSL tags cg.wic and grompp.
 # Use (1-based) indexing to uniquely reference (step_number, step_name).

examples/gromacs/cg.wic

@@ -5,35 +5,35 @@ inputs:
     - edam:format_3987
 
 steps:
-    grompp:
-      in:
-        input_top_zip_path: top_zip_path
-        config:
-          mdp:
-            integrator: cg
-            define: -DFLEXIBLE # Defines a flexible water model if it exists in the system
-            # https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html#conjugate-gradient
-            rvdw: 1.4
-            rcoulomb: 1.4
-            #coulombtype: PME
-            nsteps: 1000
-            emstep: 0.01
-            emtol: 10
-            nstxout: 100
-            nstenergy: 1
-    mdrun:
-      in:
-        nb_terms: !ii cpu  # NOTE: Workaround for a bug in gromacs 2022.2, fixed in 2022.3
-        # https://manual.gromacs.org/current/release-notes/2022/2022.3.html#energy-minimization-would-not-converge-with-gpu-and-without-dd
-        bonded_terms: !ii cpu # GPU implementation IS supported for md integrator, is NOT supported for sd integrator, etc.
-        pme_terms: !ii cpu
-        pme_fft_terms: !ii cpu
-        update_terms: !ii cpu
-    gmx_energy:
-      in:
-        config: !ii
-          terms: [Potential]
-        output_xvg_path: !ii energy_min_cg.xvg
+  grompp:
+    in:
+      input_top_zip_path: top_zip_path
+      config: !ii
+        mdp:
+          integrator: cg
+          define: -DFLEXIBLE # Defines a flexible water model if it exists in the system
+          # https://manual.gromacs.org/current/reference-manual/algorithms/energy-minimization.html#conjugate-gradient
+          rvdw: 1.4
+          rcoulomb: 1.4
+          #coulombtype: PME
+          nsteps: 1000
+          emstep: 0.01
+          emtol: 10
+          nstxout: 100
+          nstenergy: 1
+  mdrun:
+    in:
+      nb_terms: !ii cpu  # NOTE: Workaround for a bug in gromacs 2022.2, fixed in 2022.3
+      # https://manual.gromacs.org/current/release-notes/2022/2022.3.html#energy-minimization-would-not-converge-with-gpu-and-without-dd
+      bonded_terms: !ii cpu # GPU implementation IS supported for md integrator, is NOT supported for sd integrator, etc.
+      pme_terms: !ii cpu
+      pme_fft_terms: !ii cpu
+      update_terms: !ii cpu
+  gmx_energy:
+    in:
+      config: !ii
+        terms: [Potential]
+      output_xvg_path: !ii energy_min_cg.xvg
 
 wic:
   graphviz:

examples/gromacs/equil.wic

@@ -1,6 +1,6 @@
 steps:
-    nvt.wic:
-    npt.wic:
+  nvt.wic:
+  npt.wic:
 
 wic:
   graphviz:

examples/gromacs/min.wic

@@ -5,15 +5,15 @@ inputs:
     - edam:format_3987
 
 steps:
-  - steep.yml:
-      in:
-        top_zip_path: top_zip_path
+  steep.wic:
+    in:
+      top_zip_path: top_zip_path
 # Fatal error:
 # The coordinates could not be constrained. Minimizer 'cg' can not handle
 # constraint failures, use minimizer 'steep' before using 'cg'.
-  - cg.yml:
-      in:
-        top_zip_path: top_zip_path
+  cg.wic:
+    in:
+      top_zip_path: top_zip_path
 # Fatal error:
 # The combination of constraints and L-BFGS minimization is not implemented.
 # Either do not use constraints, or use another minimizer (e.g. steepest

examples/gromacs/prod.wic

@@ -11,45 +11,45 @@ inputs:
     type: float
 
 steps:
-    config_tag_mdp:
-      in:
-        nsteps: nsteps #10000
-        dt: dt #0.002
-        ref-t: ref-t #298.0
-        ref-p: ref-p #1.0
-        config: !ii
-          mdp:
-            integrator: md  # Use md for performance so we can update coordinates on GPU. Use sd for proper statistical properties.
-            rvdw: 1.0
-            rcoulomb: 1.0
-            coulombtype: PME
-            tc-grps: system
-            tau-t: 2
-            constraints: h-bonds
-            nstxout: 1000
-            nstenergy: 1000
-            pcoupl: Parrinello-Rahman
-            tau-p: 1
-            compressibility: 4.5e-5
-            comm-mode: Linear
-            comm-grps: system
-      out:
-      - output_config_string: !& config_tag_mdp_prod
-    grompp:
-      in:
-        config: !* config_tag_mdp_prod
-        input_top_zip_path: !* genion.zip  # Use the original topology file so
+  config_tag_mdp:
+    in:
+      nsteps: nsteps #10000
+      dt: dt #0.002
+      ref-t: ref-t #298.0
+      ref-p: ref-p #1.0
+      config: !ii
+        mdp:
+          integrator: md  # Use md for performance so we can update coordinates on GPU. Use sd for proper statistical properties.
+          rvdw: 1.0
+          rcoulomb: 1.0
+          coulombtype: PME
+          tc-grps: system
+          tau-t: 2
+          constraints: h-bonds
+          nstxout: 1000
+          nstenergy: 1000
+          pcoupl: Parrinello-Rahman
+          tau-p: 1
+          compressibility: 4.5e-5
+          comm-mode: Linear
+          comm-grps: system
+    out:
+    - output_config_string: !& config_tag_mdp_prod
+  grompp:
+    in:
+      config: !* config_tag_mdp_prod
+      input_top_zip_path: !* genion.zip  # Use the original topology file so
 # we don't have to question whether the topology gets messed up after file format conversions.
 # (In fact, it is not exactly identical!)
-      out:
-      - output_tpr_path: !& prod.tpr
-    mdrun:
-      in:
-        output_trr_path: !ii prod.trr # Explicitly specify for cwl_subinterpreter
-      out:
-      - output_crd_path: !& prod.gro
-      - output_trr_path: !& prod.trr
-      - output_edr_path: !& prod.edr
+    out:
+    - output_tpr_path: !& prod.tpr
+  mdrun:
+    in:
+      output_trr_path: !ii prod.trr # Explicitly specify for cwl_subinterpreter
+    out:
+    - output_crd_path: !& prod.gro
+    - output_trr_path: !& prod.trr
+    - output_edr_path: !& prod.edr
   # - cwl_subinterpreter_analysis.wic:
 
 wic:

examples/gromacs/setup_vac_min.wic

@@ -10,28 +10,28 @@ inputs:
     - edam:format_3987
 
 steps:
-  - topology.yml:
-      in:
-        crd_path: crd_path
-  - min.yml: # Minimize in vacuum first, then in solvent.
-      in:
-        top_zip_path: top_zip_path
-  - solv_ion.yml:
-      in:
-        top_zip_path: top_zip_path
+  topology.wic:
+    in:
+      crd_path: crd_path
+  min.wic: # Minimize in vacuum first, then in solvent.
+    in:
+      top_zip_path: top_zip_path
+  solv_ion.wic:
+    in:
+      top_zip_path: top_zip_path
 wic:
   graphviz:
     label: System Setup
   steps:
-    (1, topology.yml):
+    (1, topology.wic):
       wic:
         graphviz:
           label: 'Initialize\nPeriodic Box'
-    (2, min.yml):
+    (2, min.wic):
       wic:
         graphviz:
           label: 'Vacuum Minimization'
-    (3, solv_ion.yml):
+    (3, solv_ion.wic):
       wic:
         graphviz:
           label: 'Add Water\nSolvent'

examples/gromacs/solv_ion.wic

@@ -5,31 +5,32 @@ inputs:
     - edam:format_3987
 
 steps:
-  - gmx_editconf:
-      in:
-        #input_crd_path: crd_path
-        align_principal_axes: 0
-        box_type: cubic
-        distance_to_molecule: 1.2
-  - solvate:
-      in:
-        input_top_zip_path: top_zip_path
-        output_crd_path: !& solvate.gro
-        output_top_zip_path: !& solvate.zip
-  - grompp:
-      in:
-        input_crd_path: !* solvate.gro
-        input_top_zip_path: !* solvate.zip
-        config: !ii
-          maxwarn: 1 # net charge != 0
-          mdp:
-            integrator: steep
-    genion:
-      in:
-        config: !ii
-          neutral: True
-      out:
-      - output_top_zip_path: !& genion.zip
+  gmx_editconf:
+    in:
+      #input_crd_path: crd_path
+      align_principal_axes: !ii 0
+      box_type: !ii cubic
+      distance_to_molecule: !ii 1.2
+  solvate:
+    in:
+      input_top_zip_path: top_zip_path
+    out:
+    - output_crd_path: !& solvate.gro
+    -  output_top_zip_path: !& solvate.zip
+  grompp:
+    in:
+      input_crd_path: !* solvate.gro
+      input_top_zip_path: !* solvate.zip
+      config: !ii
+        maxwarn: 1 # net charge != 0
+        mdp:
+          integrator: steep
+  genion:
+    in:
+      config: !ii
+        neutral: True
+    out:
+    - output_top_zip_path: !& genion.zip
 # Use &filename to create a reference to an output. Inputs in later steps can
 # use *filename to dereference the filename and create an explicit edge.
 wic: