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- [ ] Check for GDC pipeline in nf-core or make one
- [ ] Check for trainings/workshops for learning purposes and share with the team
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### Description of the bug
I just installed the Nextflow and I am trying to do the test but I am getting the error pasted below. It's seems nextflow are trying to install Bowtie2, v. 2.4.2 but the …
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The nf-core pipeline template has these try-catch blocks to load institutional configs:
https://github.com/nf-core/tools/blob/7785b4cd8d3ce1321832e1a7ae4f2874509e31f4/nf_core/pipeline-template/next…
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The `snakemake` pipeline should be translated to `nextflow` to reach more users. Don't hesitate to comment this issue to show your interest, else we keep it as a low priority
EDIT: I'm not very fam…
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### Description of the bug
I am trying to programmatically get the list of all containers in the pipeline. However the standard command `nextflow inspect` does not seem to work, even if you tell it t…
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### Operating System
Windows 10
### Other Linux
_No response_
### Workflow Version
wf-amplicon v1.1.0
### Workflow Execution
EPI2ME Desktop (Local)
### Other workflow execution
_No response_
…
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Hi,
Whenever I run the pipeline, an error always occurs with Shovill.
When I check the .nextflow.log file, I see the following message:
10:40:30.287 [Task monitor] DEBUG nextflow.processor.Task…
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Hi!
I was trying to run the pipeline using a SMB-mounted directory in a network cluster, but I got an error at the beginning regarding symbolic links:
"Command error:
ln: failed to create sym…
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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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### Description of the bug
Hello,
Following the instructions: https://pipelines.tol.sanger.ac.uk/curationpretext/1.0.0/usage , I am getting a FileNotFound error in the most recent version of th…