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Sarek test run unable to find docker image #1519
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Hi @C2i-PeterChung, I'm afraid the latest version of Docker has some issues dealing with biocontainers. |
@maxulysse Thanks for your comment, I downgraded the docker and nextflow
Docker version 20.10.24, build 297e128 the test pipeline is work, ran successfully. but when i tried on the my samples, it isnt work again.
`Workflow execution completed unsuccessfully! The full error message was: Error executing process > 'NFCORE_SAREK:SAREK:BAM_APPLYBQSR:GATK4_APPLYBQSR (120660)' Caused by: Command executed: gatk --java-options "-Xmx3276M -XX:-UsePerfData" cat <<-END_VERSIONS > versions.yml Command exit status: Command output: Command error: Work dir: Tip: when you have fixed the problem you can continue the execution adding the option |
Description of the bug
I am new to nextlfow sarek pipeline, I tried to use docker as profile to test run the sarek pipeline but it had error. is this the docker issue ? how can I download back that bwa version, I tried to write config file to implement the bwa images but it isn't work. Please advice. Thanks.
Command used and terminal output
Relevant files
I don't have relevant files, I just followed the https://nf-co.re/docs/usage/introduction
4. To test that everything is working properly, try running the tests for your pipeline of interest in the terminal:
nextflow run nf-core/sarek -r 3.4.1 -profile test,docker --outdir test_result
System information
Liunx 5.15.0-106-generic
Distributor ID: Ubuntu
Description: Ubuntu 22.04.4 LTS
Release: 22.04
Codename: jammy
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