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Questions tagged [nextflow]

a framework for developing and managing scalable scientific data processing pipelines targeted for cloud or cluster computing

Nextflow is a framework for developing and managing scalable scientific data processing pipelines targeted for cloud or cluster computing. The framework provides a DSL that aims to extend the Unix pipe model with emphasis on functional composition, implementing a reactive dataflow programming model. To promote reproducibility, the framework supports Docker and Singularity containers.

Nextflow is developed by the Comparative Bioinformatics group at the Barcelona Center for Genomic Regulation (CRG).

It is open source software available on GitHub and distributed under the GPL3 license.

348 questions
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Try catch in Nextflow processes

How can I perform a try catch in nextflow? I am currently writing a pipeline where it is possible that the bash command I am executing exits with an exitcode 1 under certain conditions. This brings my pipeline to a grinding halt. I would now like to…
falkohof
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Nextflow tutorial getting error "no such variable"

I'm trying to learn nextflow but it's not going very well. I started with the tutorial of this site: https://www.nextflow.io/docs/latest/getstarted.html (I'm the one who installed nextflow). I copied this script : #!/usr/bin/env nextflow params.str…
Papaya
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Can I use multiple conda environments in the nextflow config?

I'm writing a pipeline in Nextflow and want to use multiple different conda (existing) environments to avoid inconsistencies in tool installation and for sharing specific modules of the pipeline. The Nextflow docs state that the best practise is to…
Ryan
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Saving the contents of a file generated inside process script into Nextflow variable

I have a Nextflow process that uses a bash script (check_bam.sh) to generate a text file. The only options for the contents of that text file are either a 0 or any other number. I would like to extract that 0 or the other value and save it to a…
Cris Tuñí
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How to call a variable created in the script in Nextflow?

I have a nextflow script that creates a variable from a text file, and I need to pass the value of that variable to a command line order (which is a bioconda package). Those two processes happen inside the "script" part. I have tried to call the…
Cris Tuñí
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Failed to create Conda environment status : 143

I am trying to run a nexflow pipeline on some data via the Linux command line, but when I do so, it fails because it fails to create the Conda environment. It looks like it tries to run the pipeline anyway, despite the environment not being set up…
user8144422
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Can you make Nextflow DAG visualisation beautiful?

Nextflow allows to efficiently make complex pipelines. Some people understand things only visually, so it's important to make a good graphical representation. Way to do so in nextflow is by -with-dag command: nextflow run -with-dag…
juststuck
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How to process multiple input (yaml/json) from S3 using Nextflow dsl2

I need to process over 1k samples with the nextflow (dsl2) pipeline in aws batch. current version of the workflow process single input per run. I'm looking workflow syntax (map tuple to iterate) to process multiple inputs to run in parralel. The…
user3214212
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Passing Python variables through Nextflow channels

I have the following simplified task and get some errors when doing it. I'm trying to get 4 letters from a string by Python and use that as a name of a new folder. My code is as follows: #!/usr/bin/env nextflow params.string="abcdefg" process…
Rossy Clair
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How to separate nested lists by element index in nextflow?

I need to separate a channel with complex list: The channel contains a nested list like this one: [1,['a','b'],['c','d']],[2,['a','b'],['e','f']] How to create two new channels so that channel one contains [[1,a,c],[2,a,e]] and channel two -…
juststuck
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Permissions error running NextFlow RNAseq test pipeline

I've been trying to run a minimal example of the NextFlow RNAseq pipeline, like so: nextflow run nf-core/rnaseq -r 3.10.0 -profile test,docker --outdir /home/kai/RNASeq/rnaseq_test/test_output However, this appears to return the error below: Error…
KLM117
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Nextflow input how to declare tuple in tuple

I am working with a nextflow workflow that, at a certain stage, groups a series of files by their sample id using groupTuple(), and resulting in a channel that looks like this: [sample_id, [file_A, file_B, ... , file_N]] [sample_id, [file_A, file_B,…
schmat_90
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Nextflow name collision

I have files with identical names but in different folders. Nextflow stages these files into the same work directory resulting in name collisions. My question is how to deal with that without renaming the files. Example: # Example data mkdir folder1…
ATpoint
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How to pass arguments to a template script being called through Nextflow

Say we call a template script from within Nextflow. How can we pass arguments to that script? For instance, a process defined like this, with no arguments, works fine: process callPython { input: path(someinput) output: …
jh_
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Nextflow combine by regex match

I have a tuple channel containing entries like: SH7794_SA119138_S1_L001, [R1.fq.gz, R2.fq.gz] And a csv split into 36 entries, each like: [samplename:SH7794_SA119138_S1, mouseID:1-4, treat:vehicle, dose:NA, time:day18, tgroup:vehicle__day18,…
varontron
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