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md_list.cwl
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md_list.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
class: Workflow
label: Example of setting up a simulation system
doc: |
CWL version of the md_list.cwl workflow for HPC.
requirements:
SubworkflowFeatureRequirement: {}
MultipleInputFeatureRequirement: {}
inputs:
step1_pdb_file: File
step2_editconf_config: string
step4_grompp_genion_config: string
step5_genion_config: string
step6_grompp_min_config: string
step8_make_ndx_config: string
step9_grompp_nvt_config: string
step11_grompp_npt_config: string
step13_grompp_md_config: string
step14_mdrun_md_config: string
outputs:
dir:
label: whole workflow output
doc: |
outputs from the whole workflow, containing these optional files:
step14_mdrun_md/output_trr_file: Raw trajectory from the free simulation step
step14_mdrun_md/output_gro_file: Raw structure from the free simulation step.
step14_mdrun_md/output_cpt_file: GROMACS portable checkpoint file, allowing to restore (continue) the
simulation from the last step of the setup process.
step13_grompp_md/output_tpr_file: GROMACS portable binary run input file, containing the starting structure
of the simulation, the molecular topology and all the simulation parameters.
step5_genion/output_top_zip_file: GROMACS topology file, containing the molecular topology in an ASCII
readable format.
type: Directory
outputSource: step15_gather_outputs/project_work_dir
steps:
step1_pdb2gmx:
label: Create Protein System Topology
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/pdb2gmx.cwl
in:
input_pdb_path: step1_pdb_file
out: [output_gro_file, output_top_zip_file]
step2_editconf:
label: Create Solvent Box
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/editconf.cwl
in:
input_gro_path: step1_pdb2gmx/output_gro_file
out: [output_gro_file]
step3_solvate:
label: Fill the Box with Water Molecules
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/solvate.cwl
in:
input_solute_gro_path: step2_editconf/output_gro_file
input_top_zip_path: step1_pdb2gmx/output_top_zip_file
out: [output_gro_file, output_top_zip_file]
step4_grompp_genion:
label: Add Ions - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step4_grompp_genion_config
input_gro_path: step3_solvate/output_gro_file
input_top_zip_path: step3_solvate/output_top_zip_file
out: [output_tpr_file]
step5_genion:
label: Add Ions - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/genion.cwl
in:
config: step5_genion_config
input_tpr_path: step4_grompp_genion/output_tpr_file
input_top_zip_path: step3_solvate/output_top_zip_file
out: [output_gro_file, output_top_zip_file]
step6_grompp_min:
label: Energetically Minimize the System - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step6_grompp_min_config
input_gro_path: step5_genion/output_gro_file
input_top_zip_path: step5_genion/output_top_zip_file
out: [output_tpr_file]
step7_mdrun_min:
label: Energetically Minimize the System - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step6_grompp_min/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file]
step8_make_ndx:
label: Generate GROMACS index file
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/make_ndx.cwl
in:
config: step8_make_ndx_config
input_structure_path: step7_mdrun_min/output_gro_file
out: [output_ndx_file]
step9_grompp_nvt:
label: Equilibrate the System (NVT) - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step9_grompp_nvt_config
input_gro_path: step7_mdrun_min/output_gro_file
input_top_zip_path: step5_genion/output_top_zip_file
input_ndx_path: step8_make_ndx/output_ndx_file
out: [output_tpr_file]
step10_mdrun_nvt:
label: Equilibrate the System (NVT) - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step9_grompp_nvt/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step11_grompp_npt:
label: Equilibrate the System (NPT) - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step11_grompp_npt_config
input_gro_path: step10_mdrun_nvt/output_gro_file
input_top_zip_path: step5_genion/output_top_zip_file
input_ndx_path: step8_make_ndx/output_ndx_file
input_cpt_path: step10_mdrun_nvt/output_cpt_file
out: [output_tpr_file]
step12_mdrun_npt:
label: Equilibrate the System (NPT) - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
input_tpr_path: step11_grompp_npt/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step13_grompp_md:
label: Free Molecular Dynamics Simulation - part 1
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/grompp.cwl
in:
config: step13_grompp_md_config
input_gro_path: step12_mdrun_npt/output_gro_file
input_top_zip_path: step5_genion/output_top_zip_file
input_ndx_path: step8_make_ndx/output_ndx_file
input_cpt_path: step12_mdrun_npt/output_cpt_file
out: [output_tpr_file]
step14_mdrun_md:
label: Free Molecular Dynamics Simulation - part 2
run: biobb/biobb_adapters/cwl/biobb_md/gromacs/mdrun.cwl
in:
config: step14_mdrun_md_config
input_tpr_path: step13_grompp_md/output_tpr_file
out: [output_trr_file, output_gro_file, output_edr_file, output_log_file, output_cpt_file]
step15_gather_outputs:
label: Archiving outputs to be returned to user
in:
external_project_file: step1_pdb_file
external_files:
source:
- step14_mdrun_md/output_trr_file
- step14_mdrun_md/output_gro_file
- step14_mdrun_md/output_cpt_file # we have to run with v1.2.0, or this null value breaks the workflow!
- step13_grompp_md/output_tpr_file
- step5_genion/output_top_zip_file
linkMerge: merge_flattened
pickValue: all_non_null # this is needed to avoid null values causing problems, but is only available from v1.2.0 onwards
run: md_gather.cwl
out: [project_work_dir]