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Hello, I have been encountering a recurring error while performing call-methylation:
`'entries: 43715, qc fail: 0, could not calibrate: 0, no alignment: 43715, bad reads: 43710.'`
The analysis p…
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# Issue Report
## Please describe the issue:
Hi, I am trying to re-align sequencing results from an adaptive sampling experiment. So I want to run dorado aligner on the fastq_pass/ directory
Th…
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While running following command
nextflow run main_AMR++.nf -profile conda
N E X T F L O W ~ version 24.04.3
Launching `main_AMR++.nf` [elegant_gauss] DSL2 - revision: f6bfe39b99
A M R …
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### Ask away!
Hello,
I ran a prepared library of 9 rAAV samples on a MinION flowcell and would like to use the wf-aav-qc workflow to analyze the fastq data. I have successfully used the workflow …
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### Description of the bug
I want to run workflow with `params.save_analysis_ready_fastqs = true`. When I pass this in local configuration file, [my.zip](https://github.com/user-attachments/files/16…
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**Is your feature request related to a problem? Please describe.**
Projects with many samples can produce a large amount of data in one measurement.
To analyse effects only observed in a subset of…
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Reported by @beatrizsavinhas
Analyses for cases in which `data_delivery` includes `fastq` or `analysis` still receive an `uploaded_at` date even when the rsync job fails. Effectively, the upload fa…
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### Ask away!
Hello,
I am trying to get the demo model to work using the following script on HPC and I get a couple of error Plus 4 more processes waiting for tasks…
Doing reference based transcr…
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Hi, I am using stringMLST and I noticed that I got different results for running the same sample more than once. The database changed (updated). What was surprising that some of the assigned ST's in t…
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### Description of the bug
Hi,
I have been using nf-core/rnasq for a long time, but with the update of Nextflow, I am receiving the following error messages. I downloaded my fastq files with asper…