NMR pipe - CWL workflow for NMR spectra Peak Picking

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CWL_dem1_NMR_Peak_Picking

CWL workflow for NMR spectra Peak Picking
The workflow takes as input a series of 2D 1H 15N HSQC NMR spectra and uses nmrpipe tools to convert the spectra in nmrpipe format and performs an automatic peak picking.
This test uses a protein MDM2 with different ligands and peptide and generates a peak list with 1H and 15N chemical shift values for each spectrum. The difference among these peak lists can be used to characterize the ligand binding site on the protein.
Test

Install cwl-runner
Install docker
run cwl-runner nmrpipe_workflow.cwl nmrpipe_workflow.yml

The steps contained in the workflow are the following:

bruker_to_script : It reads Bruker files format and creates the "convertion script"
script_to_fid : runs the "convertion script" in order to convert the data to nmrpipe free formats
fid_to_pipe : executes FFT and autophasing on nmrpipe data
pipe_to_pick : executes nmrpipe peak-piking algorithm

Code Snippets

baseCommand: [sh, runBrukerToScript.sh]
hints:
  DockerRequirement:
    # dockerPull: tlinnet/relax
    dockerPull: andreagia/nmrpipecwl

CWL From line 3 of master/brucker_to_script.cwl

- entryname: runBrukerToScript.sh
  entry: |
      cp $1/ser* .
      cp $1/acqus .
      cp $1/acqu?s ./
      cp $1/pulseprogram ./
      bruker -auto -notk
      ls

CWL bruker From line 15 of master/brucker_to_script.cwl

baseCommand: [/bin/csh, runProcessFid.sh]
hints:
  DockerRequirement:
    # dockerPull: tlinnet/relax
    dockerPull: andreagia/nmrpipecwl

CWL From line 3 of master/fid_to_pipe.cwl

- entryname: runProcessFid.sh
  entry: |
    #cwl doesn't set correclty docker user 
    #in order to work set the right env
    source /opt/software/NMRPipe/com/nmrInit.linux212_64.com
    basicFT2.com -xP0 auto -yP0 90 -list > nmr.com
    csh nmr.com

CWL NMR From line 16 of master/fid_to_pipe.cwl

baseCommand: [sh, runPick.sh]
hints:
  DockerRequirement:
    # dockerPull: tlinnet/relax
    dockerPull: andreagia/nmrpipecwl

CWL From line 3 of master/pipe_to_pick.cwl

- entryname: runPick.sh
  entry: |
      #cp -r $1/fid ./
      #chmod -R 664 $1/fid
      #basicFT2.com -xP0 -82 -xEXTX1 10.4ppm -xEXTXN 5.4ppm -list > test.com
      #sh test.com
      #ls -lh
      pkDetect2D.tcl -in test.ft2

CWL From line 15 of master/pipe_to_pick.cwl

baseCommand: [sh, runScriptToFid.sh]
hints:
  DockerRequirement:
    # dockerPull: tlinnet/relax
    dockerPull: andreagia/nmrpipecwl

CWL From line 3 of master/script_to_fid.cwl

- entryname: runScriptToFid.sh
  entry: |
      ls
      cp $1/ser* .
      cp $1/acqus .
      cp $1/acqu?s ./
      cp $1/pulseprogram ./
      # cp $1/fid.com ./ # to comment if the script is part of the workflow
      sh fid.com
      ls