Nextflow good first issues

This issue proposes adding support for RNA sequencing data by incorporating a subworkflow that utilizes the STAR aligner. The implementation can be adapted from the existing nf-core/rnaseq pipeline. This is marked as a "help wanted" and "good first issue," suggesting it's a good entry point for new contributors.

This issue proposes adding a new parameter to Viralrecon to allow users to specify a minimum depth for calling bases and variants. This would provide more flexibility in variant calling and consensus generation, and the request also suggests updating the metric table to reflect this new minimum depth.

This feature request aims to refactor several Nextflow modules to remove the use of `task.ext` fields for parameters that are not essential overrides. The goal is to simplify module inputs by treating these fields as standard parameters instead of relying on the `task.ext` mechanism.

This issue proposes adding a new visualization to the MultiQC report that displays taxonomic classifications of contigs. The goal is to have a stacked bar chart similar to existing read-level classifications, ideally incorporating a metric for completeness.

This issue proposes adding an optional feature to the viral metagenome pipeline. When enabled, the pipeline will utilize host-filtered FASTQ files for downstream mapping and polishing steps if they are available, rather than the original clean FASTQ files. This aims to reduce runtime and storage requirements for large datasets.

This issue proposes creating a custom annotation database leveraging the NCBI Virus database and JenaDB. The goal is to build a specialized resource for virus annotations.

This issue proposes adding support for Metabuli, a tool that classifies metagenomic reads by comparing them to reference genomes using both amino acid and nucleotide comparisons. The goal is to integrate this functionality into the existing project.

This issue requires updating nf-core modules used in nf-core/eager to include a 'versions' topic. Some modules can be updated automatically using `nf-core modules update`, while others may require manual intervention or upstream fixes.

This issue tracks the migration of the `amulety/esm2` module to use topic channels. It's part of a larger effort to standardize module organization and includes a checklist for completion, such as updating tests and configuration files.

This issue tracks the migration of the `amulety/balmpaired` module to use topic channels. It's part of a larger meta-issue and requires updating the module, ensuring tests pass, modifying `meta.yml`, and passing nf-core lint checks. The 'good first issue' label suggests it's intended for newcomers.

This issue tracks the migration of the `amulety/antiberty` module to use topic channels. It serves as a sub-task for a larger meta-issue and requires updating the module, ensuring tests pass, modifying `meta.yml`, and verifying nf-core lint compliance. The "good first issue" label suggests it's intended for newcomers.

This issue tracks the migration of the `amulety/antiberta2` module to use topic channels. It serves as a tracking ticket for the process, referencing a parent meta-issue and a migration guide, and includes a checklist for completion.

The user is inquiring if the nf-core/smrnaseq pipeline supports the analysis of small RNA biotypes beyond miRNAs, such as piRNAs, tRNAs, and rRNAs. They are seeking guidance on how to perform such analyses if supported, or recommendations for alternative workflows if not.

This issue proposes packaging additional functions from the blobtoolkit library, specifically `blobtoolkit/blobdir` and `blobtoolkit/windowstats`, as individual nf-core modules. This would allow users to leverage these specific tools within their own Nextflow pipelines without needing to run the entire sanger-tol pipeline.

The user wants to enable the nf-co2footprint plugin by default in machine configuration profiles. A test is currently preventing this, citing that plugin definitions are only allowed at the top-most config scope. The user is questioning the reasoning behind this restriction and seeking a way to include plugins in their desired configuration.

This issue proposes to standardize the naming convention of normalized variant files generated by different tools. Currently, one tool outputs files with a '.normalised.vcf.gz' suffix, while another uses '.norm.vcf.gz'. The suggested solution is to adjust the configuration of the latter tool to match the former's naming.

This issue is part 5 of a larger effort to adopt topic channels across all nf-core modules. It lists a significant number of modules that need to be updated to use topic channels, indicating a systematic refactoring task. The goal is to improve the organization and maintainability of the nf-core modules.

This feature request aims to expand the capabilities of scverse-related modules within the nf-core/modules repository. Currently, these modules only support the h5ad file format for input and output. The user proposes adding support for the zarr file format, which has seen significant improvements in recent development.