I am developing a nextflow based pipeline, I have two processes for downloading files which are given below, process templateExample{ publishDir "data_analysis_files", mode:'copy' output: path "*_gex.csv" , emit: count_files script: ''' "download_files.sh" ''' } process read_count_p{ publishDir "results",mode:'copy' input: path…
I am defining two nextflow processes. The first one, scatter(), creates two files. Then, parallel() is spawned twice, once for each file. Here is my setup. // bug.nf nextflow.enable.dsl = 2 workflow { main: scatter(params.config) scatter.out.configs | flatten | parallel…
I'm trying to request a VM with 128Gb of memory through nextflow, but it keeps failing. I can request VMs with 64Gb, but I get the following errors when I try to request more: Nextflow stdout: ERROR ~ Error executing…
I want to run my Nextflow pipeline using an AWS Batch executor. However, I pushed a private (not public) image to Dockerhub. When executing the Nextflow pipeline locally, I can access the local image. However, when executing my Nextflow pipeline…
I've created a docker image using the following Dockerfile: FROM ubuntu:18.04 ARG DEBIAN_FRONTEND=noninteractive WORKDIR /usr/local/src # Setting up general environment RUN apt-get -y update && apt-get install -y build-essential && apt-get install -y wget && apt-get install -y hmmer &&…
Hi Please find below a nf script and a config file. I have run them on two computers. Both computers have nextflow (v 22.04.5) and docker installed. However, one computer shows an error message. Please see the screenshot attached. I…