How to indicate to nextlow where takes output?











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I have a script in python which save a file in a specific directory.



For example this code named "write.py":



with open("project/results/txt/output.txt", "w") as f:

    f.write("this is a txt file")


So I execute my script in "project/src" and the output of this script is in "project/results/txt/".



Here an example of a script Nextflow in "project/":



process writeTxt{

    output:

    file "output.txt"



    """

    python3 ../../../src/write.py 

    """

}


"../../../" ==> to go out of work directory



But nextflow return that it didn't find "projet/results/txt/output.txt".



So how indicates to Nextflow where is the output of a script?






nextflow







share|improve this question


























    up vote
    0
    down vote

    favorite












    I have a script in python which save a file in a specific directory.



    For example this code named "write.py":



    with open("project/results/txt/output.txt", "w") as f:
    
    f.write("this is a txt file")


    So I execute my script in "project/src" and the output of this script is in "project/results/txt/".



    Here an example of a script Nextflow in "project/":



    process writeTxt{
    
    output:
    
    file "output.txt"
    

    
    """
    
    python3 ../../../src/write.py 
    
    """
    
}


    "../../../" ==> to go out of work directory



    But nextflow return that it didn't find "projet/results/txt/output.txt".



    So how indicates to Nextflow where is the output of a script?






    nextflow







    share|improve this question
























      up vote
      0
      down vote

      favorite









      up vote
      0
      down vote

      favorite











      I have a script in python which save a file in a specific directory.



      For example this code named "write.py":



      with open("project/results/txt/output.txt", "w") as f:
      
    f.write("this is a txt file")


      So I execute my script in "project/src" and the output of this script is in "project/results/txt/".



      Here an example of a script Nextflow in "project/":



      process writeTxt{
      
    output:
      
    file "output.txt"
      

      
    """
      
    python3 ../../../src/write.py 
      
    """
      
}


      "../../../" ==> to go out of work directory



      But nextflow return that it didn't find "projet/results/txt/output.txt".



      So how indicates to Nextflow where is the output of a script?






      nextflow







      share|improve this question













      I have a script in python which save a file in a specific directory.



      For example this code named "write.py":



      with open("project/results/txt/output.txt", "w") as f:
      
    f.write("this is a txt file")


      So I execute my script in "project/src" and the output of this script is in "project/results/txt/".



      Here an example of a script Nextflow in "project/":



      process writeTxt{
      
    output:
      
    file "output.txt"
      

      
    """
      
    python3 ../../../src/write.py 
      
    """
      
}


      "../../../" ==> to go out of work directory



      But nextflow return that it didn't find "projet/results/txt/output.txt".



      So how indicates to Nextflow where is the output of a script?






      nextflow




      nextflow






      share|improve this question













      share|improve this question











      share|improve this question




      share|improve this question










      asked Nov 21 at 16:33









      Adam Bellaïche

      105




      105
























          1 Answer
          1






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          oldest

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          up vote
          0
          down vote



          accepted










          This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.






          share|improve this answer





















          • How Can I declare this? I don't know the way to do that.
            – Adam Bellaïche
            Nov 21 at 17:12










          • because I started Nextflow last week.
            – Adam Bellaïche
            Nov 22 at 8:21













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          1 Answer
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          active

          oldest

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          1 Answer
          1






          active

          oldest

          votes









          active

          oldest

          votes






          active

          oldest

          votes








          up vote
          0
          down vote



          accepted










          This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.






          share|improve this answer





















          • How Can I declare this? I don't know the way to do that.
            – Adam Bellaïche
            Nov 21 at 17:12










          • because I started Nextflow last week.
            – Adam Bellaïche
            Nov 22 at 8:21

















          up vote
          0
          down vote



          accepted










          This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.






          share|improve this answer





















          • How Can I declare this? I don't know the way to do that.
            – Adam Bellaïche
            Nov 21 at 17:12










          • because I started Nextflow last week.
            – Adam Bellaïche
            Nov 22 at 8:21















          up vote
          0
          down vote



          accepted







          up vote
          0
          down vote



          accepted






          This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.






          share|improve this answer












          This is an anti-pattern. Nextflow tasks are expected to produce and consume files in task execution directory. If such output file is produced by a upstream task, that must be declared as task output to make it accessible in the task work directory.







          share|improve this answer












          share|improve this answer



          share|improve this answer










          answered Nov 21 at 16:56









          pditommaso

          1,01021429




          1,01021429












          • How Can I declare this? I don't know the way to do that.
            – Adam Bellaïche
            Nov 21 at 17:12










          • because I started Nextflow last week.
            – Adam Bellaïche
            Nov 22 at 8:21




















          • How Can I declare this? I don't know the way to do that.
            – Adam Bellaïche
            Nov 21 at 17:12










          • because I started Nextflow last week.
            – Adam Bellaïche
            Nov 22 at 8:21


















          How Can I declare this? I don't know the way to do that.
          – Adam Bellaïche
          Nov 21 at 17:12




          How Can I declare this? I don't know the way to do that.
          – Adam Bellaïche
          Nov 21 at 17:12












          because I started Nextflow last week.
          – Adam Bellaïche
          Nov 22 at 8:21






          because I started Nextflow last week.
          – Adam Bellaïche
          Nov 22 at 8:21




















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