Fix prettier linting issues and code review feedback

- Remove unused METAPHLAN_UNKNOWN_LIST import from workflow
- Fix typo: 'fasterqc-dump' -> 'fasterq-dump'
- Remove global singularity.enabled to avoid container engine conflicts
- Format markdown files with prettier (CODE_OF_CONDUCT, README, REFACTORING_SUMMARY)
- Add .prettierignore to exclude Nextflow/Groovy files and pre-existing files

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>

Author: Copilot

.prettierignore

@@ -0,0 +1,13 @@
+# Ignore Nextflow and Groovy files (no parser available)
+*.nf
+*.config
+
+# Ignore existing files from before refactoring
+docker/cloudbuild.yaml
+nextflow_schema.json
+unitn_setup.md
+
+# Ignore build artifacts and dependencies
+work/
+.nextflow*
+results/

CODE_OF_CONDUCT.md

@@ -17,23 +17,23 @@ diverse, inclusive, and healthy community.
 Examples of behavior that contributes to a positive environment for our
 community include:
 
-* Demonstrating empathy and kindness toward other people
-* Being respectful of differing opinions, viewpoints, and experiences
-* Giving and gracefully accepting constructive feedback
-* Accepting responsibility and apologizing to those affected by our mistakes,
+- Demonstrating empathy and kindness toward other people
+- Being respectful of differing opinions, viewpoints, and experiences
+- Giving and gracefully accepting constructive feedback
+- Accepting responsibility and apologizing to those affected by our mistakes,
   and learning from the experience
-* Focusing on what is best not just for us as individuals, but for the
+- Focusing on what is best not just for us as individuals, but for the
   overall community
 
 Examples of unacceptable behavior include:
 
-* The use of sexualized language or imagery, and sexual attention or
+- The use of sexualized language or imagery, and sexual attention or
   advances of any kind
-* Trolling, insulting or derogatory comments, and personal or political attacks
-* Public or private harassment
-* Publishing others' private information, such as a physical or email
+- Trolling, insulting or derogatory comments, and personal or political attacks
+- Public or private harassment
+- Publishing others' private information, such as a physical or email
   address, without their explicit permission
-* Other conduct which could reasonably be considered inappropriate in a
+- Other conduct which could reasonably be considered inappropriate in a
   professional setting
 
 ## Enforcement Responsibilities
@@ -106,7 +106,7 @@ Violating these terms may lead to a permanent ban.
 ### 4. Permanent Ban
 
 **Community Impact**: Demonstrating a pattern of violation of community
-standards, including sustained inappropriate behavior,  harassment of an
+standards, including sustained inappropriate behavior, harassment of an
 individual, or aggression toward or disparagement of classes of individuals.
 
 **Consequence**: A permanent ban from any sort of public interaction within

README.md

@@ -38,7 +38,6 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
-
    - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`.
    - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
    - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.
@@ -65,6 +64,7 @@ The samplesheet should be a tab-separated file with the following columns:
 - `NCBI_accession`: SRA accession number(s), separated by semicolons for multiple runs
 
 For local FASTQ files (with `--local_input`):
+
 - `sample_id`: Unique sample identifier
 - `file_paths`: Path(s) to FASTQ file(s), separated by semicolons for multiple files
 
@@ -127,17 +127,21 @@ Multiple profiles can be specified by separating them with a comma.
 ### Main arguments
 
 #### `--input`
+
 Path to input samplesheet (TSV format). This replaces the older `--metadata_tsv` parameter.
 
 #### `--outdir`
+
 The output directory where the results will be saved. You must use absolute paths to storage on Cloud infrastructure.
 
 #### `--local_input`
+
 Set to `true` to provide local FASTQ file paths instead of downloading from SRA.
 
 Default: `false`
 
 #### `--skip_humann`
+
 Skip HUMAnN functional profiling step.
 
 Default: `false`
@@ -152,26 +156,31 @@ The pipeline will automatically download and cache reference databases in the lo
 - Human and mouse reference genomes for KneadData
 
 #### `--store_dir`
+
 Directory to store reference databases.
 
 Default: `'databases'`
 
 #### `--metaphlan_index`
+
 MetaPhlAn database index version.
 
 Default: `'latest'`
 
 #### `--chocophlan`
+
 ChocoPhlAn database version for HUMAnN.
 
 Default: `'full'`
 
 #### `--uniref`
+
 UniRef database version for HUMAnN.
 
 Default: `'uniref90_diamond'`
 
 #### `--organism_database`
+
 Organism reference database for KneadData contamination removal.
 
 Options: `'human_genome'`, `'mouse_C57BL'`
@@ -207,15 +216,19 @@ If you use seandavi/curatedmetagenomicsnextflow for your analysis, please cite t
 ### Pipeline tools
 
 - [MetaPhlAn](https://github.com/biobakery/MetaPhlAn)
+
   > Blanco-Míguez A, Beghini F, Cumbo F, et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat Biotechnol. 2023;41(11):1633-1644. doi:10.1038/s41587-023-01688-w
 
 - [HUMAnN](https://github.com/biobakery/humann)
+
   > Beghini F, McIver LJ, Blanco-Míguez A, et al. Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. eLife. 2021;10:e65088. doi:10.7554/eLife.65088
 
 - [KneadData](https://github.com/biobakery/kneaddata)
+
   > The KneadData tool is part of the bioBakery suite of tools for metagenomic analysis.
 
 - [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
   > Di Tommaso P, Chatzou M, Floden EW, et al. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017;35(4):316-319. doi:10.1038/nbt.3820
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

REFACTORING_SUMMARY.md

@@ -11,6 +11,7 @@ The pipeline has been successfully refactored from a monolithic structure to a m
 ### 1. Directory Structure
 
 **Before:**
+
 ```
 curatedMetagenomicsNextflow/
 ├── main.nf (800+ lines)
@@ -20,6 +21,7 @@ curatedMetagenomicsNextflow/
 ```
 
 **After:**
+
 ```
 curatedMetagenomicsNextflow/
 ├── main.nf (73 lines)
@@ -80,49 +82,57 @@ All processes have been extracted into individual modules:
 13. **HUMANN** - Functional profiling
 
 Each module includes:
+
 - `main.nf` - Process definition
 - `meta.yml` - Module metadata and documentation (for key modules)
 
 ### 3. Configuration Improvements
 
 #### conf/base.config
+
 - Defines base process settings
 - Implements resource labels (process_single, process_low, process_medium, process_high)
 - Includes check_max() function for resource management
 - Standard error handling strategies
 
 #### conf/modules.config
+
 - Module-specific configurations
 - PublishDir settings per module
 - Extension arguments support
 
 #### conf/test.config
+
 - Minimal test dataset configuration
 - Resource limits for CI/CD
 - Skip computationally expensive steps
 
 ### 4. Parameter Standardization
 
 **New nf-core standard parameters:**
+
 - `--input` (replaces `--metadata_tsv`)
 - `--outdir` (replaces `--publish_dir`)
 - `--publish_dir_mode` (replaces `--publish_mode`)
 - `--max_cpus`, `--max_memory`, `--max_time`
 - `--help`, `--version`
 
 **Backwards compatibility maintained:**
+
 - `--metadata_tsv` still works (maps to `--input`)
 - `--publish_dir` still works (maps to `--outdir`)
 
 ### 5. Workflow Structure
 
 **New workflow file:** `workflows/curatedmetagenomicsnextflow.nf`
+
 - Clean separation of concerns
 - Reusable helper functions
 - Improved readability
 - Better maintainability
 
 **Updated main.nf:**
+
 - Minimal entry point
 - Parameter validation
 - Help message
@@ -131,6 +141,7 @@ Each module includes:
 ### 6. Documentation
 
 #### README.md
+
 - Comprehensive usage guide
 - Installation instructions
 - Parameter documentation
@@ -139,33 +150,39 @@ Each module includes:
 - Quick start examples
 
 #### CHANGELOG.md
+
 - Version history
 - Detailed change log
 - Migration guide
 
 #### CITATIONS.md
+
 - All tool citations
 - Proper attribution
 - DOI links
 
 #### CODE_OF_CONDUCT.md
+
 - Community standards
 - Contributor guidelines
 
 #### Module meta.yml files
+
 - Input/output specifications
 - Tool descriptions
 - Keywords and authors
 
 ### 7. CI/CD
 
 #### .github/workflows/ci.yml
+
 - Automated testing
 - Multiple Nextflow versions
 - Stub run testing
 - Profile testing
 
 #### .github/workflows/linting.yml
+
 - Code quality checks
 - nf-core lint
 - Pre-commit hooks
@@ -175,6 +192,7 @@ Each module includes:
 ### 8. Container Management
 
 Enhanced container support:
+
 - Docker profile
 - Singularity profile
 - Podman support
@@ -208,16 +226,19 @@ nextflow run . -profile test,docker --outdir results
 For users of the previous version:
 
 ### Old Command:
+
 ```bash
 nextflow run main.nf --metadata_tsv samples.tsv --publish_dir results
 ```
 
 ### New Command (recommended):
+
 ```bash
 nextflow run seandavi/curatedmetagenomicsnextflow --input samples.tsv --outdir results -profile docker
 ```
 
 ### Backwards Compatible:
+
 ```bash
 nextflow run seandavi/curatedmetagenomicsnextflow --metadata_tsv samples.tsv --publish_dir results
 ```
@@ -246,6 +267,7 @@ nextflow run seandavi/curatedmetagenomicsnextflow --metadata_tsv samples.tsv --p
 ## Validation
 
 The refactored pipeline:
+
 - ✅ Maintains all original functionality
 - ✅ Follows nf-core directory structure
 - ✅ Uses nf-core parameter conventions
@@ -258,6 +280,7 @@ The refactored pipeline:
 ## Next Steps
 
 Future enhancements could include:
+
 1. Creating subworkflows for related processes (e.g., METAPHLAN_PROFILE)
 2. Adding more module metadata files
 3. Implementing input validation schema

nextflow.config

@@ -138,9 +138,7 @@ weblog {
     url = 'https://nf-telemetry-819875667022.us-central1.run.app/nextflow-telemetry/events'
 }
 
-// Container configuration - enabled by default with singularity
-singularity.enabled = true
-singularity.pullTimeout = '2h'
+// Container configuration
 process.container = 'docker://seandavi/curatedmetagenomics:metaphlan4.1.0'
 
 profiles {

workflows/curatedmetagenomicsnextflow.nf

@@ -9,7 +9,6 @@ include { LOCAL_FASTQC                  } from '../modules/local/local_fastqc/ma
 include { KNEADDATA                     } from '../modules/local/kneaddata/main'
 include { INSTALL_METAPHLAN_DB          } from '../modules/local/install_metaphlan_db/main'
 include { METAPHLAN_UNKNOWN_VIRUSES_LISTS } from '../modules/local/metaphlan_unknown_viruses_lists/main'
-include { METAPHLAN_UNKNOWN_LIST        } from '../modules/local/metaphlan_unknown_list/main'
 include { METAPHLAN_MARKERS             } from '../modules/local/metaphlan_markers/main'
 include { SAMPLE_TO_MARKERS             } from '../modules/local/sample_to_markers/main'
 include { CHOCOPHLAN_DB                 } from '../modules/local/chocophlan_db/main'