Sarai Varona

### Description of feature When no .gff file for annotation is given to the pipeline, the ivar_variants_to_vcf step is not performing well during the codon merging. Also, the script should...

Variant calling isn't run when using --skip_asciigenome with metagenomic data

2

### Description of the bug When I run the pipeline with the param --skip_asciigenome, variant calling steps won't be performed. ### Command used and terminal output ```console # Command used:...

Added option to add a custom annotation and clarified multiQC results

1

Included [issue #390](https://github.com/nf-core/viralrecon/issues/390) and issue #336 enhancements - Added new param to add a custom annotation (gtf or gff format) - Added new subworkflow to perform the additional annotation -...

### Description of feature In cutadapt module for primer sequence trimming, in de novo assembly subworkflow, primer sequences are given as -A and -a by default: https://github.com/nf-core/viralrecon/blob/3731dd3a32a67a2648ea22c2bd980c224abdaee2/modules/local/cutadapt.nf#L25 It would be...

### Description of feature We are working on a custom gtf file with multiple overlapping features for SARS-CoV-2, but viralrecon won't let you use a gtf file as annotation file....

My group and I have been reviewing the [Proposed Standards for Public Health Bioinformatics Software](https://github.com/pha4ge/pipeline-resources/blob/main/docs/pipeline-standards.md) document from the perspective of a team dedicated to the development of analysis pipelines, and...

Changed Cutadapt to use nf-core modules

1

Fixes issue #409 ## PR checklist - [X] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should...

Sometimes, mapping founds a plasmid, but then BLAST doesn't find any contig matching the plasmid to generate the summary, and plasmidID crushes with: ```bash CREATING SUMMARY REPORT (Fri Jul 12...

### Description of the bug Add serializer in the collect_statistics_information function to be able to use labels when getting stats. https://github.com/BU-ISCIII/iskylims/blob/ff3571110f4974bb08fa3d5fdb70d7b5000d821f/wetlab/api/utils/sample.py#L513 ### Command used and terminal output ```console ``` ###...

### Description of the bug There is a problem with `nf-core modules lint` when working with patched modules that require different inputs or outputs compared to the original module. Steps...