Update to Nextclade v3 and Enhancement of Coverage and Depth Analysis

[tives82]

Changes and modifications proposed in this Pull Request:

• Nextclade Modules Updates:
  Updated the NEXTCLADE_VARIABLES, NEXTCLADE_DATASETGET, and NEXTCLADE_RUN modules to Nextclade version 3.0 to leverage the latest enhancements and bug fixes.

• New Modules for Segment Coverage Analysis found in the assembly_typing_clade_variables subworkflow:
  IRMA_SEGMENT_COVERAGE: Calculates reference length, sequence length, and percent coverage for each segment for a given sample. Output files are placed in the ‘irma_segment_coverage’ directory.
  MERGE_COVERAGE_RESULTS: Aggregates coverage data across all samples into merged_coverage_results.tsv file placed in the ‘irma_segment_coverage’ directory.

• New Modules for Read Mapping Analysis found in the assembly_typing_clade_variables subworkflow:
  SAMTOOLS_MAPPED_READS: Calculates the number of reads mapped and mean depth for each segment for a given sample. Output files are placed in the ‘samtools_mapped_reads’ directory.
  MERGE_BAM_RESULTS: Aggregates depth analysis data across all samples into merged_bam_results.tsv file placed in the ‘samtools_mapped_reads’ directory.

• Report Generation found in the assembly_typing_clade_variables subworkflow:
  MERGE_BAM_COVERAGE_RESULTS: This module compiles a comprehensive report from the merged_bam_results.tsv and merged_coverage_results.tsv files. The final report, merged_bam_coverage_results.tsv, is placed in the ‘SUMMARY_REPORTS’ directory.

• Configuration Fixes:
  Corrected the manifest version within nextflow.config to resolve the "Wrong version printed at runtime" issue.

• Additional Notes:
  The documentation has been updated to reflect these changes.

[github-actions]

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[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit aaf2ffe

+| ✅  16 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

• pipeline_todos - TODO string in meta.yml: #Add a description of all of the variables used as input
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

❔ Tests ignored:

• files_exist - files_exist
• nextflow_config - nextflow_config
• files_unchanged - files_unchanged
• actions_awstest - actions_awstest
• multiqc_config - multiqc_config
• modules_structure - modules_structure

✅ Tests passed:

• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (127 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• schema_params - Schema matched params returned from nextflow config
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json

Run details

• nf-core/tools version 2.7.2
• Run at 2024-03-14 17:26:39

[erinyoung]

Is

unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

worrisome?

This prints out when I ran the workflow using your test profile.

Also, you probably want to remove something from your config file because there's this warning:

WARN: Undocumented setting `docker.userEmulation` is not supported any more - please remove it from your config

[jwarnn]

I reviewed the code changes and didn't see any issues and I ran a test run which produced the expected output.