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### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

mribeirodantas

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

mribeirodantas

### Have you checked the docs? - [x] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) - [x] [nf-core modules documentation](https://nf-co.re/docs/contributing/modules) ### Description of the bug One of the optional outputs (`chr_statistics`) looks for the...

lbeltrame

The gprofiler2 module outputs were missing the actual gene names/IDs in the expected columns, making it impossible to identify which specific genes contribute to pathway enrichment. Expected behavior: *.gprofiler2.all_enriched_pathways.tsv should...

mohe1linux

Data submissions to ENA can be made using the Webin command line submission interface (Webin-CLI). https://bioconda.github.io/recipes/ena-webin-cli/README.html Docs: https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html Using in seqsubmit pipeline

KateSakharova

new subworkflow: fastq_remove_adapters_and_merge

1

### Is there an existing subworkflow for this? - [x] I have searched for the existing subworkflow ### Is there an open PR for this? - [x] I have searched...

vagkaratzas

edmundmiller

new module: vembrane

2

### Is there an existing module for this? - [x] I have searched for the existing module ### Is there an open PR for this? - [x] I have searched...

famosab

update module: vcf2zarr/convert

2

## PR checklist Closes #9268 by adding index file to tests - [x] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug...

camlloyd

Fix: Quote shell parameters

3

https://github.com/nf-core/differentialabundance/pull/444 I ran a differential abundance pipeline with a study name that had spaces in it, and the pipeline crashed because the `make_app_from_files.R` caller script was not escaping parameters as...

zeehio