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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
scw_input_pdb_path: File
outputs:
gnuplot_output_png_file:
type: File
outputSource: gnuplot/gnuplot_output_png_file
rms_output_xvg_file:
type: File
outputSource: rmsd/rms_output_xvg_file
md_output_gro_file:
type: File
outputSource: equilibration/md_output_gro_file
md_output_trr_file:
type: File
outputSource: equilibration/md_output_trr_file
steps:
mutate_structure:
run: scwrl.cwl
in:
scw_input_pdb_path: scw_input_pdb_path
out: [scw_output_pdb_file]
create_topology:
run: pdb2gmx.cwl
in:
p2g_input_structure_pdb_path: mutate_structure/scw_output_pdb_file
out: [p2g_output_gro_file, p2g_output_top_zip_file]
create_water_box:
run: editconf.cwl
in:
ec_input_gro_path: create_topology/p2g_output_gro_file
out: [ec_output_gro_file]
solvate:
run: solvate.cwl
in:
sol_input_solute_gro_path: create_water_box/ec_output_gro_file
sol_input_top_zip_path: create_topology/p2g_output_top_zip_file
out: [sol_output_gro_file, sol_output_top_zip_file]
ions_preprocess:
run: grompp.cwl
in:
step:
default: gppions
gpp_input_gro_path: solvate/sol_output_gro_file
gpp_input_top_zip_path: solvate/sol_output_top_zip_file
gpp_input_mdp_path:
default:
class: File
location: ../workflows/mdp/gmx_full_ions_test.mdp
out: [gpp_output_tpr_file]
add_ions:
run: genion.cwl
in:
gio_input_tpr_path: ions_preprocess/gpp_output_tpr_file
gio_input_gro_path: solvate/sol_output_gro_file
gio_input_top_zip_path: solvate/sol_output_top_zip_file
out: [gio_output_gro_file, gio_output_top_zip_file]
minimization_preprocess:
run: grompp.cwl
in:
step:
default: gppmin
gpp_input_gro_path: add_ions/gio_output_gro_file
gpp_input_top_zip_path: add_ions/gio_output_top_zip_file
gpp_input_mdp_path:
default:
class: File
location: ../workflows/mdp/gmx_full_min_test.mdp
out: [gpp_output_tpr_file]
minimization:
run: mdrun.cwl
in:
step:
default: mdmin
md_input_tpr_path: minimization_preprocess/gpp_output_tpr_file
out: [md_output_gro_file, md_output_trr_file]
nvt_dynamics_preprocess:
run: grompp.cwl
in:
step:
default: gppnvt
gpp_input_gro_path: minimization/md_output_gro_file
gpp_input_top_zip_path: add_ions/gio_output_top_zip_file
gpp_input_mdp_path:
default:
class: File
location: ../workflows/mdp/gmx_full_nvt_test.mdp
out: [gpp_output_tpr_file]
nvt_dynamics:
run: mdrun.cwl
in:
step:
default: mdnvt
md_input_tpr_path: nvt_dynamics_preprocess/gpp_output_tpr_file
out: [md_output_gro_file, md_output_trr_file, md_output_cpt_file]
npt_dynamics_preprocess:
run: grompp.cwl
in:
step:
default: gppnpt
gpp_input_gro_path: nvt_dynamics/md_output_gro_file
gpp_input_top_zip_path: add_ions/gio_output_top_zip_file
gpp_input_cpt_path: nvt_dynamics/md_output_cpt_file
gpp_input_mdp_path:
default:
class: File
location: ../workflows/mdp/gmx_full_npt_test.mdp
out: [gpp_output_tpr_file]
npt_dynamics:
run: mdrun.cwl
in:
step:
default: mdnpt
md_input_tpr_path: npt_dynamics_preprocess/gpp_output_tpr_file
out: [md_output_gro_file, md_output_trr_file, md_output_cpt_file]
equilibration_preprocess:
run: grompp.cwl
in:
step:
default: gppeq
gpp_input_gro_path: npt_dynamics/md_output_gro_file
gpp_input_top_zip_path: add_ions/gio_output_top_zip_file
gpp_input_cpt_path: npt_dynamics/md_output_cpt_file
gpp_input_mdp_path:
default:
class: File
location: ../workflows/mdp/gmx_full_md_test.mdp
out: [gpp_output_tpr_file]
equilibration:
run: mdrun.cwl
in:
step:
default: mdeq
md_input_tpr_path: equilibration_preprocess/gpp_output_tpr_file
out: [md_output_gro_file, md_output_trr_file, md_output_cpt_file]
rmsd:
run: rms.cwl
in:
rms_input_gro_path: equilibration/md_output_gro_file
rms_input_trr_path: equilibration/md_output_trr_file
out: [rms_output_xvg_file]
gnuplot:
run: gnuplot.cwl
in:
gnuplot_input_xvg_path: rmsd/rms_output_xvg_file
out: [gnuplot_output_png_file]
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