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## Bug report
When users try to run [this pipeline](https://github.com/sanger-bentley-group/GBS-Typer-sanger-nf) with Singularity, it works on Nextflow 22.10.7 and before, but fails on Nextflow 23…
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### Description of feature
Hello,
Thank you for developing this fantastic pipeline. I am currently trying to use it to process my RNAseq data (human).
This is the command I used:
```
nextflow…
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## Bug report
### Expected behavior and actual behavior
I would anticipate that passing arguments such as `--minimap2_args '-k15'` would result in the parameter `minimap2_args` being set to t…
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### Description of the bug
I am trying to run the pipeline on the HPC PDC-Dardel and get error messages that I am not able to make sense of. I post it here in case you have any tips on how to figure …
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When looking at the list of NAO repos, I always find it hard to remember which of 'mgs-workflow' or 'mgs-pipeline' is which. @jeffkaufman uses 'v1 pipeline' and 'v2 pipeline' to distinguish them. Perh…
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Hi,
I got this error
```
> nextflow run WarrenLab/minigraph-cactus-nf -profile lorencm --seqFile ../seqFile.txt --reference AU --binariesMode singularit
cactus-minigraph: error: unrecognized argum…
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Hi
Hi
I am running RepeatMaker nextflow using a custom TE library on a genome assembly. All processes worked successfully unless the last process (combineRMAlignOutput) with the following error (I…
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## New feature
It does not seem like there is a perfect way of picking up existing files and any new files from a root path using a combination of the two channel factories - `watchPath` and `fromP…
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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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### Description of feature
Dear developers,
I do have two questions:
1. I want to pass several databases to BTK's nextflow pipeline (v0.6.0) should I pass them several times using --busco li…