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Hello!
I was trying to set up MetaPhage-0.3.3 and I ran into an error when working on the demo test example. I was unsure why there seems to be a problem with memory when the resources seem to be a…
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## New feature
In order for Nextflow to play nicely in managed environments, we need to avoid using `System.exit` calls, and the recently depreciated `exit()` Nextflow function.
For problems wit…
ewels updated
11 months ago
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Is there a relation between image file size and memory usage. - check vs a report. In which case we could use dynamic allocation
https://nextflow-io.github.io/patterns/conditional-resources/
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### Description of the bug
--limitBAMsortRAM cannot be set by --star_options '--limitBAMsortRAM 800000000000', it can only be set by custom config, which override any other existing config.
I've a…
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Hi there,
I am trying to run the pipeline on some older fastq files (circa 2010s) using the docker profile. The reads for the files are relatively short at ~75bp. Following previous advice from Abh…
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Hello,
I am running CalliNGS workflow using AWS BATCH on AWS Sagemaker using AWS s3 storage drives. I am using the following containerOverides:
```
containerOverrides={
'command': [
…
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A nextflow pipeline that runs a comparative genomic analysis to understand the gene expansions and contractions for a selection of species
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There isn't much context provided with the following error
```
$ nextflow run main.nf \
-profile docker \
--genome GRCh38 \
--digestion arima \
--input '/home/ec2-user/*{1,2}.fastq.gz'…
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- DESeq2 demo
- Genome and fastq download from NCBI (download tools)
- Running Nextflow by pointing to main.nf or to a github repo (and explanation)
- Add a resume exercise and optional flags
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The job query status logic needs to be revamped in order to work well with Tower.
As of now, the jobs (on Tower) are always shown as running and are not progressing to completed status. Despite be…