Getting an output value from a python script within nextflow process

[Dave Deandre]

Hi,

Is there a way to output a value initialized from within python code block in a nextflow process so it can be stored in a channel?

For instance, here is my code:

process getFirstMinimumCoverage {

       input:

               file coverageInfo from coverageFileChannel

       output:

               val firstMinPair into firstMinPairChannel

       script:

               """

                #!/usr/bin/env python

                sampleName = "$coverageInfo".replace(".ctx.covg","")

                fh = open("$coverageInfo", "r")

                pairsList = []

                for line in fh:

                        line = line.strip()

                        pairsList.append(line.split("\t"))

                fh.close()

                firstMinPair = pairsList[2]

                for i in range(2,len(pairsList) - 2):

                        if int(pairsList[i][1]) < int(pairsList[i+1][1]):

                                firstMinPair = pairsList[i]

                                break

                """

}

Nextflow errors the following statement in the s

Caused by:

  Missing value declared as output parameter: firstMinPair

Thank you in advance!

Dave

[Marc Logghe]

Hi Dave,

As far as I know it is not possible to access python variables from NextFlow. The only way to get hands on that value is to print it in your python script and grab that with NextFlow from the stdout.

Then, in your process:

output:

               stdout into firstMinPairChannel

HTH,

Marc

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[Steve]

Similarly, consider writing the output value to a file then setting that file as the 'output' of the task, then you can read the contents of the file from within your Channel and pass on the value.

[Dave Deandre]

Hi Marc,

Thank you for the suggestion, now I am using this method to output the value.

Best,

Dave

[Dave Deandre]

Hi Steve,

I think the standard out value works better for me, but I will keep in mind of this method in the future. Thanks for the help!

Dave