Questions tagged [nextflow]

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How to execute several processes sequentially, without channels?

Using DSL2. I have processes A, B, C which I want to run in sequence - B waits for A to finish, C waits for B to finish. They are not communicating via channels so I can't do A.out.collect(). I have ...
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62 views

Nextflow: How to initialize channel from CSV file but only after CSV file created?

Process A runs a python script which generates a CSV file in some absolute file path say "/mnt/x/blah.csv". Process B needs to consume the CSV file line by line, after process A has finished....
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Passing around complex metadata in Nextflow

I have a number of samples (from the 1000 genomes) that I want to analyse using Nextflow. However, I need to keep track of their metadata, fields like sample ID, analysis type etc. So I have a basic ...
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Nextflow: Why does non-local reference to $projectDir break hash stability and hence break task cache?

I have a process like the following: ...
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191 views

parse csv/text file to create a channel with array in nextflow

[![example csv file][1]][1] First I want to start by parsing and doing some operation on a text/csv file. How could I read a csv/text file in nextflow? Suppose, I have above csv file with 3 columns. ...
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1answer
139 views

nextflow: Filter outputs of a process

How could I filter outputs of a process in the input of the next process? Filtering works fine in channel, but if I try to filter outputs I got compilation error. I tried as follows: ...