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Please convert each of this as an issue when you start working on one.
(That can be done by clicking on the circle dot `⊙` at the end of the line in the list below, hover on a list item to see it)
A…
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When running a stub run for testing pipelines, some tools (such as `ANTs`) return an `exit code status 1` when calling the help script. Example:
```bash
Test [91f130a6] 'Connectomics + tracking pr…
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Module to run plink --genome to calculate identity-by-descent
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### Description of the bug
I am having trouble getting the following test to work. Any clues to what I am doing wrong.
The command I ran was:
nextflow run nf-core/scrnaseq -profile test,docker --o…
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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Add nf-core module to both ``genome`` only and ``genome_and_annotation`` subworkflows.
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**CPU:** AMD Ryzen Threadripper 2950X
**OS:** Gentoo Linux
**Kernel:** 6.10.0-pf4-x86_64
**Desktop:** Hyprland (Wayland)
**GPUs:** NVIDIA GeForce GTX 970 (primary), NVIDIA GeForce RTX 2070
**Driv…
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### Description of feature
I started a sarek run (`v3.4.2`) providing a custom reference in the form of a bgzipped FASTA. The run from FASTQs started normally and did not run into any errors until th…
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### Description of the bug
I have been able to successfully run the pipeline test
nextflow run nf-core/differentialabundance \
--outdir test \
-profile test,docker
Unfortunately, I remain u…
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### Description of the bug
Hello,
I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.
Previously, I have executed the pipeline without the G…