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nf-amazon does not exist #992

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JiahuaQu opened this issue Apr 12, 2023 · 0 comments
Closed

nf-amazon does not exist #992

JiahuaQu opened this issue Apr 12, 2023 · 0 comments
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bug Something isn't working

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@JiahuaQu
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JiahuaQu commented Apr 12, 2023

Description of the bug

Hi, I created a conda virtual environment where I installed both nextflow (version: 22.10.6) and nf-core (version: 2.7.2). Then I downloaded nf-core/sarek (version: 3.1.2) Singularity. However, when I ran the sarek pipeling, Plugin with id nf-amazon did not exist in any repository. Later, I downloaded the plugin nf-amazon-1.16.1.zip from the website (https://github.com/nextflow-io/nf-amazon/releases/download/1.16.1/nf-amazon-1.16.1.zip) directly and specified it in the coding, but the pipeline still didn't recognize the plugin. Ask your help to solve this problem occuring when running the sarek Singularity in HPC (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC)). Thank you very much.

Command used and terminal output

log=./08-test_NextFlow-nf-core-sarek/test-01/my.log

workflow=./08-test_NextFlow-nf-core-sarek/nf-core-sarek-3.1.2/workflow

profile=singularity

input=./08-test_NextFlow-nf-core-sarek/test_data/samplesheet.csv

outdir=./08-test_NextFlow-nf-core-sarek/test-01/output

plugin=./08-test_NextFlow-nf-core-sarek/nf-core-sarek-3.1.2/plugins/nf-amazon-1.16.1

# run pipeline
nextflow -log $log run $workflow -profile $profile --input $input --outdir $outdir --genome GATK.GRCh38 -plugins $plugin

Relevant files

nf-amazon-1.16.1.zip
my.log
my2.log

System information

Linux version 3.10.0-1160.88.1.el7.x86_64 ([email protected]) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-44) (GCC) ) #1 SMP Tue Mar 7 15:41:52 UTC 2023

@JiahuaQu JiahuaQu added the bug Something isn't working label Apr 12, 2023
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