Describe the bug
Upgraded WSL2 and docker. When Performing a test install run, the pipeline stops and states unable to find image 'quay.io/biocontainers/fastqc:0.11.9--0' locally
Impact
Unable to run test install
To Reproduce
Steps to reproduce the behavior:
What environment you are running the pipeline in (i.e. HPC, local, cloud etc). Local
What version of the pipeline you are using v2.0.0
The command that was run to cause the error nextflow run cdcgov/phoenix -r v2.0.0 -profile docker,test -entry PHOENIX --kraken2db /mnt/p/Sequencing/
If you used a custom config file please provide it
The text of the error itself - screenshots are great for this!
Include the files that caused the error
(if the file(s) contains something you don't want public open an issue with a brief description AND then email HAISeq@cdc.gov with the title QH ISSUE # so we can track the problem. DO NOT send PII!
Expected behavior
clean run of pipeline
Screenshots
Logs
If applicable, please attach logs to help describe your problem. These would be the .command.err, .command.out, .command.sh and/or the .nextflow.log files associated with the run/process that failed. The .nextflow.log file is in directory you ran the pipeline from. The .command.XXX files are found in <directory you ran pipeline from>/work/XX/xxxxxxxxxxxxxx here the x and X are a random string of letters/numbers associated with the process. As the pipeline runs on CLI you will see the beginning of these strings to the left of the process that is running.
Additional context
Add any other context about the problem here. If you have done any internet sleuthing already please link to any relevant posts on the topic.
jvhagey
commented
3 months ago
Describe the bug Upgraded WSL2 and docker. When Performing a test install run, the pipeline stops and states unable to find image 'quay.io/biocontainers/fastqc:0.11.9--0' locally
Impact Unable to run test install
To Reproduce Steps to reproduce the behavior:
What environment you are running the pipeline in (i.e. HPC, local, cloud etc). Local
What version of the pipeline you are using v2.0.0
The command that was run to cause the error nextflow run cdcgov/phoenix -r v2.0.0 -profile docker,test -entry PHOENIX --kraken2db /mnt/p/Sequencing/
If you used a custom config file please provide it
The text of the error itself - screenshots are great for this!
Include the files that caused the error
Expected behavior clean run of pipeline
Screenshots
Logs If applicable, please attach logs to help describe your problem. These would be the
.command.err,.command.out,.command.shand/or the.nextflow.logfiles associated with the run/process that failed. The.nextflow.logfile is in directory you ran the pipeline from. The.command.XXXfiles are found in<directory you ran pipeline from>/work/XX/xxxxxxxxxxxxxxhere the x and X are a random string of letters/numbers associated with the process. As the pipeline runs on CLI you will see the beginning of these strings to the left of the process that is running.Additional context Add any other context about the problem here. If you have done any internet sleuthing already please link to any relevant posts on the topic.