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First run of the workflow (e.g. new system or user) with singularity involves pulling multiple container images from docker hub. This can fail likely due to race conditions in singularity.
https:/…
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Singularity is a virtualization layer, like Docker, which is friendly with HPC systems.
At least on my current cluster the core libraries (glib, kernel, etc.), are a bit aged, and some software (si…
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It would be good to add some functionality to cluster the inferred ASVs into OTUs based on a pairwise identity threshold.
This can be particularly useful for interpretting assignments that were mad…
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Hi!
I'm bringing this issue over from [gitter](https://gitter.im/nf-tower/community?at=6179fc69a41fd206990c2040).
I haven't been able to execute docker-based workflows with Tower on the `Google …
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Hi, great work with the pipeline.
Unfortunately, my university does not allow docker on the HPC, but they will whitelist and install Singularity/Apptainer images on request.
Can I just point the…
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Setup CI via Github Actions, Travis CI, CircleCI or some other service.
Small test dataset run with test profile using Conda profile.
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I pulled the container from docker hub.
I my nextflow.config I have this:
container = 'staphb/pilon'
I ran pilon :
java -Xmx16G -jar "pilon-1.24.jar"
pilon --genome ...
But I got this error …
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As @junjun-zhang suggest, we could add `-offline` option when run `nextflow run`.
In our case, we don't really need nextflow to check github once a particular version of the workflow code is pulled…
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samtools version 1.9
trim_galore version 0.6.4_dev (dependency fastqc and cudadapt v. 2.8)
biscuit version 0.3.8.20180515
bamtools version 2.5.1
picard version 2.18.15-snapshot
wgbs_tools = gith…
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Hej Lukas, jag vill uppdatera dig på läget:
Läget just nu är att jag bekantat mig med och installerat nextflow på min dator, läst scipopartikeln och försökt läsa forskningsartikeln och tittat på in…