Nextflow good first issues

The user wants to reduce the number of files published from alevin-fry's output to save storage space and speed up data transfer, as they are primarily interested in the count matrix and quant.json. They suggest making the publishing of intermediate files optional, as these are still available in the working directory.

This issue identifies a problem in Nextflow test files where fixture files are created by directly writing to the source tree (`moduleDir`) or outside the work directory (`launchDir`). This leads to untracked files and incorrect task input tracking. The proposed solution is to use `channel.of(...).collectFile()` to generate these fixtures within the Nextflow channel, ensuring proper tracking and management.

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 phased genome assembly capabilities to the `genomeassembler`. It suggests exploring strategies like using HI-C reads or parental short-reads with tools like `hifiasm`, or alternatively, phasing long-reads using `longcallD` with a reference before assembly.

This issue proposes adding CI test output assemblies to the `nf-core/test-datasets` repository. The goal is to enable testing of the 'assembly-as-input' functionality, which is currently advertised but not verified, potentially leading to undiscovered bugs.

This issue proposes enhancing test coverage for a pipeline's later stages, as current tests only cover core assembly functionality. The goal is to implement more detailed nf-test tests that account for sample-level parameterization, which has previously led to bugs being discovered late in the full test runs.

This issue proposes adding Illumina short-read genomic data to both the Continuous Integration (CI) and full test runs. The goal is to ensure comprehensive testing with this type of data, using SRR1604937 as a reference for compatibility with existing test data.

This issue proposes adding support for the `--alleles` flag in GATK's Mutect2 tool. This feature would enable users to specify a reference VCF file, allowing Mutect2 to force-call variants present in that reference file within the sample being analyzed.

This issue requests the inclusion of BUSCO lineages as a comma-separated string within the report. This enhancement aims to make the lineage information easily copy-pastable for users.

This issue requests adding the TaxonID to the Assembly report. The TaxonID is already collected by the assembly pipeline and is needed for blobtoolkit, making this an enhancement to the report's utility.

This issue proposes the development of a new PNG display plugin for JBrowse. The goal is to allow curators to generate and display genome-wide images on demand, which are currently produced by separate scripts. The developer believes this should be a straightforward implementation.

The reporting module's Quarto (`qmd`) files are functional but difficult to maintain due to iterative development and a lack of initial polish. This issue seeks to clean up the R templates, improve internal consistency, and optimize the report generation process.

This issue proposes adding SyRi, a tool for visualizing structural variations, to the genome assembler's quality control pipeline. The goal is to complement existing QC by comparing assemblies against a reference, with potential for both per-stage and combined analysis. The proposer has existing SyRi pipelines and R-based plotting implementations that could be ported.

This issue proposes integrating or replacing the `ragtag/patch` module within the `ASSEMBLE` subworkflow with `quickmerge`. The goal is to evaluate `quickmerge`'s performance, potentially starting with a switch to allow for comparison before a full replacement. The author is seeking contributors to implement this enhancement.

This issue requests the implementation of coverage statistics in the genome browser's summary view. Currently, coverage is displayed as 'NaN' or 'undefined'. The proposed solution is to calculate coverage by dividing the total read length by the genome size and to properly display this metric.

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 the addition of a new module for 'CRABS' to the nf-core/modules repository. The primary goal is to port existing crabs modules from nf-core/readsimulator, specifically focusing on extending them with new functions from v1.0.7 onwards. The immediate need is to implement the `crabs/merge` submodule to address an open pull request.

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 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.