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Questions tagged [nextflow]

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Master of Pores Installation Mac OS Mojave 10.14

I'm bit of a newbie with ONT analyses and am having some trouble with the Master Of Pores installation instructions ( I've managed to install ...
guray00's user avatar
  • 11
0 votes
1 answer

nextflow `fromPath` not passing all files with * is #!/usr/bin/env nextflow params.input = '' tchan = Channel.fromFile(params.input) tchan.println() I have a.bam, b.bam and c.bam I run: ...
aerijman's user avatar
  • 585
1 vote
0 answers

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 ...
Migwell's user avatar
  • 360
4 votes
2 answers

Run Nextflow with file dependencies inside a Docker container?

I’m trying to run a Nextflow workflow in a custom Docker container. Without Docker, the workflow succeeds. But running it inside the container leads to an error because a dependent file cannot be ...
Konrad Rudolph's user avatar
3 votes
2 answers

Autodetect max number of cores and pass as an argument in Nextflow

I am creating a pipeline in Nextflow. One step is creating a pangenome with Roary. Roary takes threads as an argument and if no number of threads is supplied as an argument it defaults to one. Is ...
TW93's user avatar
  • 439