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The Nextflow pipeline run instructions can be simplified by using a conda environment file (`conda_env.yaml`):
```
name: sicelore-2.1
channels:
- bioconda
- conda-forge
- defaults
depen…
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1. Create one container with all dependencies
Pipeline:
1. cmalign query sequences to 16s profile
2. esl-alimerge query and reference alignments
3. pplacer
4. guppy classifications classificati…
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### Description of feature
Dear Georgie,
The most recent version of Parabricks includes Minimap2, and I need to run simple Minimap jobs, but I am having trouble using Parabricks on Gadi. Rather th…
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### Description of the bug
Issue with latest Nextflow release.
This was a silent message before, it's now an error and fails the pipeline.
### Command used and terminal output
_No response_
### Re…
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### Description of the bug
Pipeline execution:
- Initial run: Failed, error reported missing .pgen file.
- Rerun with '-resume': Same error occurred.
1. Versions: Nextflow 24.04.4, Java 11.0.2…
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HITE is already a series of modules (https://github.com/CSU-KangHu/HiTE), but we could add this either as a sub workflow,, or for now just a module with the main command.
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## Bug report
### Expected behavior and actual behavior
Error strategy should be respected, but when a process fails due to running out of walltime, the whole pipeline is terminated.
### Ste…
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Hi, I tried to build the ICEfinder container today, but ran into the following errors:
1) I had to remove the first line from icefinder-v1.0-local.def (although the ICEfinder_linux.tar.gz exists)
`W…
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Hi! I can't tell if there are any previous reports of this error, because I can't seem to see any other issues on the Github.
I recently ran a screen with the Zuber lab's 2-guide human library, usi…
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Hi. My process got stopped due to a temporary storage issue. I sorted out that issue. And then when I try to run the script again with the -resume command, it first gives me the 'report.overwrite' iss…