Add MAGMA as --mode magma (pinned to v0.3.0; version-isolated; experimental)

[abhi18av]

Add MAGMA as the second analysis mode (--mode magma)

Integrates the TORCH-consortium/magma nf-core port (from mycobactopia-org/MAGMA, branch nf-core-tbanalyzer) into the tbanalyzer meta-pipeline as the second bundled pipeline, after MTBseq (--mode mtbseq, #17).

Warning

MAGMA mode is experimental / not yet biologically validated. The full Docker run (GATK/VQSR/phylogeny) is deferred to a follow-up. --mode mtbseq is unaffected. Draft until the MAGMA Docker test is green.

Design principle: version-isolated, orchestration-only

Each bundled pipeline may need different versions of the same tools, so tbanalyzer does not dedup/share modules and does not modify the pipelines' logic — it only facilitates execution. MAGMA's complete module set is vendored under a magma-scoped path with its own container pins:

• modules/local/magma/ (17 custom modules) + modules/local/magma/nf-core/ (24 nf-core module copies at MAGMA's own versions — not sharing tbanalyzer's modules/nf-core/{gatk4,samtools,bcftools,fastqc,…})
• subworkflows/local/magma/ (7), workflows/magmanf.nf (entry workflow MAGMA), bin/ (15 scripts), data/magma-references/ (~28 MB H37Rv + VQSR truth VCFs + GVCF panel + SnpEff DB)

Wiring

• main.nf dispatches --mode magma → MAGMA; mode enum + magma_options schema group (61 params, all magma_-namespaced; tool *_path params dropped)
• Mode-gated conf/magma_base.config + conf/magma_modules.config; test_magma profile + conf/magma_test.config (3 downsampled M. tuberculosis samples on Zenodo, doi 10.5281/zenodo.20671479)
• assets/schema_input.json uses anyOf so the shared input schema accepts both the mtbseq (sample,fastq_1) and MAGMA-native (Sample,R1) samplesheet shapes; MAGMA self-validates its own CSV

Upstream fixes (made on mycobactopia-org/MAGMA, then re-vendored)

Completed gaps in the in-progress nf-core-module migration: GATK_MARK_DUPLICATES_DELLY call (.out → .out.bam), and def prefix/def annotationPrefix in two stub blocks. Port nextflow lint is clean; the MAGMA DAG now compiles.

Validation

• Config parses (strict v2) for both modes; samplesheet validates; full MAGMA DAG compiles & schedules.
• -stub-run can't fully exercise MAGMA (its workflow does splitJson() on validator output, which stubs leave empty — a stub-mode limitation). Biological validation = the deferred Docker run.

dev → master is the intended release flow.

[github-actions]

nf-core pipelines lint overall result: Failed ❌

Posted for pipeline commit 86aa9d2

+| ✅ 208 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗ 103 tests had warnings |!
-| ❌  97 tests failed       |-

Details

❌ Test failures:

• nextflow_config - Default value from the Nextflow schema params.magma_input_samplesheet = samplesheet.magma.csv`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_vcf_name = joint`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_ref_fasta_basename = NC-000962-3-H37Rv`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_use_ref_gvcf = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_median_coverage = 10.0`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_breadth_of_coverage = 0.9`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_rel_abundance = 0.7`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_ntm_fraction = 0.2`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_site_representation = 0.95`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_cutoff_strand_bias = 0.0`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_only_validate_fastqs = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_merge_analysis = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_variant_recalibration = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_base_recalibration = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_minor_variants_gatk = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_phylogeny_and_clustering = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_complex_regions = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_ntmprofiler = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_tbprofiler_fastq = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_spotyping = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_rdanalyzer = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_skip_ismapper = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_iqtree_standard_bootstrap = True`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_iqtree_fast_ml_only = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_iqtree_fast_bootstrapped_phylogeny = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_iqtree_accurate_ml_only = False`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_snpeff_genome_id = Mycobacterium_tuberculosis_h37rv`` not found in nextflow.config.
• nextflow_config - Default value from the Nextflow schema params.magma_should_publish_bam = False`` not found in nextflow.config.
• schema_params - Default value for param magma_input_samplesheet invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_vcf_name invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_basename invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_dir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_fai invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_dict invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_amb invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_ann invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_bwt invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_pac invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_sa invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_gb invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_fasta_rdanalyzer invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_use_ref_gvcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_gvcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_ref_gvcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_dbsnp_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_dbsnp_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_benavente2015_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_benavente2015_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_coll2014_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_coll2014_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_coll2018_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_coll2018_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_napier2020_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_napier2020_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_walker2015_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_walker2015_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_zeng2018_vcf invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_zeng2018_vcf_tbi invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_excluded_loci_list invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_rrna_list invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_drgenes_list invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_queries_multifasta invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_median_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_breadth_of_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_rel_abundance invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_ntm_fraction invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_site_representation invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_cutoff_strand_bias invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_only_validate_fastqs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_merge_analysis invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_variant_recalibration invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_base_recalibration invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_minor_variants_gatk invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_phylogeny_and_clustering invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_complex_regions invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_ntmprofiler invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_tbprofiler_fastq invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_spotyping invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_rdanalyzer invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_skip_ismapper invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_iqtree_standard_bootstrap invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_iqtree_fast_ml_only invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_iqtree_fast_bootstrapped_phylogeny invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_iqtree_accurate_ml_only invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_snpeff_genome_id invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_snpeff_config_file invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_snpeff_db_dir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param magma_should_publish_bam invalid: Not in pipeline parameters. Check nextflow.config.
• container_configs - conf/containers_conda_lock_files_amd64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_conda_lock_files_arm64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_docker_amd64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_docker_arm64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_singularity_https_amd64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_singularity_https_arm64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_singularity_oras_amd64.config is out of date – please regenerate the container configuration files.
• container_configs - conf/containers_singularity_oras_arm64.config is out of date – please regenerate the container configuration files.

❗ Test warnings:

• readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
• pipeline_todos - TODO string in README.md: TODO nf-core:
• pipeline_todos - TODO string in README.md: Include a figure that guides the user through the major workflow steps. Many nf-core
• pipeline_todos - TODO string in README.md: Fill in short bullet-pointed list of the default steps in the pipeline 1. Read QC (FastQC)2. Present QC for raw reads (MultiQC)
• pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
• pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
• pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
• pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
• pipeline_todos - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• pipeline_todos - TODO string in nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
• pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
• pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
• pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
• pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
• pipeline_todos - TODO string in CONTRIBUTING.md: Add any pipeline specific contribution guidelines here, such as coding styles, procedures, checklists etc.
• pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in gatk4.nf: If in doubt look at other nf-core/modules to see how we are doing things! :)
• pipeline_todos - TODO string in gatk4.nf: A module file SHOULD only define input and output files as command-line parameters.
• pipeline_todos - TODO string in gatk4.nf: Software that can be piped together SHOULD be added to separate module files
• pipeline_todos - TODO string in gatk4.nf: Optional inputs are not currently supported by Nextflow. However, using an empty
• pipeline_todos - TODO string in gatk4.nf: List required Conda package(s).
• pipeline_todos - TODO string in gatk4.nf: See section in main README for further information regarding finding and adding container addresses to the section below.
• pipeline_todos - TODO string in gatk4.nf: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
• pipeline_todos - TODO string in gatk4.nf: Where applicable please provide/convert compressed files as input/output
• pipeline_todos - TODO string in gatk4.nf: Named file extensions MUST be emitted for ALL output channels
• pipeline_todos - TODO string in gatk4.nf: List additional required output channels/values here
• pipeline_todos - TODO string in gatk4.nf: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
• pipeline_todos - TODO string in gatk4.nf: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
• pipeline_todos - TODO string in gatk4.nf: If the tool supports multi-threading then you MUST provide the appropriate parameter
• pipeline_todos - TODO string in gatk4.nf: Please replace the example samtools command below with your module's command
• pipeline_todos - TODO string in gatk4.nf: Please indent the command appropriately (4 spaces!!) to help with readability ;)
• pipeline_todos - TODO string in gatk4.nf: A stub section should mimic the execution of the original module as best as possible
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
• pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
• schema_params - Schema param magma_input_samplesheet not found from nextflow config
• schema_params - Schema param magma_vcf_name not found from nextflow config
• schema_params - Schema param magma_ref_fasta_basename not found from nextflow config
• schema_params - Schema param magma_ref_fasta_dir not found from nextflow config
• schema_params - Schema param magma_ref_fasta not found from nextflow config
• schema_params - Schema param magma_ref_fasta_fai not found from nextflow config
• schema_params - Schema param magma_ref_fasta_dict not found from nextflow config
• schema_params - Schema param magma_ref_fasta_amb not found from nextflow config
• schema_params - Schema param magma_ref_fasta_ann not found from nextflow config
• schema_params - Schema param magma_ref_fasta_bwt not found from nextflow config
• schema_params - Schema param magma_ref_fasta_pac not found from nextflow config
• schema_params - Schema param magma_ref_fasta_sa not found from nextflow config
• schema_params - Schema param magma_ref_fasta_gb not found from nextflow config
• schema_params - Schema param magma_ref_fasta_rdanalyzer not found from nextflow config
• schema_params - Schema param magma_use_ref_gvcf not found from nextflow config
• schema_params - Schema param magma_ref_gvcf not found from nextflow config
• schema_params - Schema param magma_ref_gvcf_tbi not found from nextflow config
• schema_params - Schema param magma_dbsnp_vcf not found from nextflow config
• schema_params - Schema param magma_dbsnp_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_benavente2015_vcf not found from nextflow config
• schema_params - Schema param magma_benavente2015_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_coll2014_vcf not found from nextflow config
• schema_params - Schema param magma_coll2014_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_coll2018_vcf not found from nextflow config
• schema_params - Schema param magma_coll2018_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_napier2020_vcf not found from nextflow config
• schema_params - Schema param magma_napier2020_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_walker2015_vcf not found from nextflow config
• schema_params - Schema param magma_walker2015_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_zeng2018_vcf not found from nextflow config
• schema_params - Schema param magma_zeng2018_vcf_tbi not found from nextflow config
• schema_params - Schema param magma_excluded_loci_list not found from nextflow config
• schema_params - Schema param magma_rrna_list not found from nextflow config
• schema_params - Schema param magma_drgenes_list not found from nextflow config
• schema_params - Schema param magma_queries_multifasta not found from nextflow config
• schema_params - Schema param magma_cutoff_median_coverage not found from nextflow config
• schema_params - Schema param magma_cutoff_breadth_of_coverage not found from nextflow config
• schema_params - Schema param magma_cutoff_rel_abundance not found from nextflow config
• schema_params - Schema param magma_cutoff_ntm_fraction not found from nextflow config
• schema_params - Schema param magma_cutoff_site_representation not found from nextflow config
• schema_params - Schema param magma_cutoff_strand_bias not found from nextflow config
• schema_params - Schema param magma_only_validate_fastqs not found from nextflow config
• schema_params - Schema param magma_skip_merge_analysis not found from nextflow config
• schema_params - Schema param magma_skip_variant_recalibration not found from nextflow config
• schema_params - Schema param magma_skip_base_recalibration not found from nextflow config
• schema_params - Schema param magma_skip_minor_variants_gatk not found from nextflow config
• schema_params - Schema param magma_skip_phylogeny_and_clustering not found from nextflow config
• schema_params - Schema param magma_skip_complex_regions not found from nextflow config
• schema_params - Schema param magma_skip_ntmprofiler not found from nextflow config
• schema_params - Schema param magma_skip_tbprofiler_fastq not found from nextflow config
• schema_params - Schema param magma_skip_spotyping not found from nextflow config
• schema_params - Schema param magma_skip_rdanalyzer not found from nextflow config
• schema_params - Schema param magma_skip_ismapper not found from nextflow config
• schema_params - Schema param magma_iqtree_standard_bootstrap not found from nextflow config
• schema_params - Schema param magma_iqtree_fast_ml_only not found from nextflow config
• schema_params - Schema param magma_iqtree_fast_bootstrapped_phylogeny not found from nextflow config
• schema_params - Schema param magma_iqtree_accurate_ml_only not found from nextflow config
• schema_params - Schema param magma_snpeff_genome_id not found from nextflow config
• schema_params - Schema param magma_snpeff_config_file not found from nextflow config
• schema_params - Schema param magma_snpeff_db_dir not found from nextflow config
• schema_params - Schema param magma_should_publish_bam not found from nextflow config
• schema_description - No description provided in schema for parameter: mtbseq_user

❔ Tests ignored:

• nextflow_config - Config default ignored: params.mtbseq_ref_and_indexes_path
• nextflow_config - Config default ignored: params.mtbseq_resilist
• nextflow_config - Config default ignored: params.mtbseq_intregions
• nextflow_config - Config default ignored: params.mtbseq_categories
• nextflow_config - Config default ignored: params.mtbseq_basecalib
• nf_test_content - nf_test_content

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/nf-test.yml
• files_exist - File found: .github/actions/get-shards/action.yml
• files_exist - File found: .github/actions/nf-test/action.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-tbanalyzer_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/CONTRIBUTING.md
• files_exist - File found: docs/images/nf-core-tbanalyzer_logo_light.png
• files_exist - File found: docs/images/nf-core-tbanalyzer_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: nf-test.config
• files_exist - File found: tests/default.nf.test
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: conf/igenomes_ignored.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: ro-crate-metadata.json
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: docs/images/nf-core-tbanalyzer_logo.png
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/NfcoreTemplate.groovy
• files_exist - File not found check: lib/Utils.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: lib/WorkflowMain.groovy
• files_exist - File not found check: lib/WorkflowTbanalyzer.groovy
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: pipeline_template.yml
• files_exist - File not found check: Singularity
• files_exist - File not found check: lib/nfcore_external_java_deps.jar
• files_exist - File not found check: .travis.yml
• nextflow_config - Found nf-schema plugin
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config variable (correctly) not found: params.max_cpus
• nextflow_config - Config variable (correctly) not found: params.max_memory
• nextflow_config - Config variable (correctly) not found: params.max_time
• nextflow_config - Config variable (correctly) not found: params.validationFailUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: params.validationLenientMode
• nextflow_config - Config variable (correctly) not found: params.validationSchemaIgnoreParams
• nextflow_config - Config variable (correctly) not found: params.validationShowHiddenParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedParams
• nextflow_config - Config variable (correctly) not found: validation.failUnrecognisedHeaders
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: 1.0dev
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• nextflow_config - nextflow.config contains configuration profile test
• nextflow_config - Config default value correct: params.mode= mtbseq
• nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
• nextflow_config - Config default value correct: params.custom_config_version= master
• nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Config default value correct: params.publish_dir_mode= copy
• nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
• nextflow_config - Config default value correct: params.validate_params= true
• nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
• nextflow_config - Config default value correct: params.mtbseq_path= MTBseq
• nextflow_config - Config default value correct: params.mtbseq_minbqual= 13
• nextflow_config - Config default value correct: params.mtbseq_mincovf= 4
• nextflow_config - Config default value correct: params.mtbseq_project= mtbseqnf
• nextflow_config - Config default value correct: params.mtbseq_minphred= 4
• nextflow_config - Config default value correct: params.mtbseq_minfreq= 75
• nextflow_config - Config default value correct: params.mtbseq_unambig= 95
• nextflow_config - Config default value correct: params.mtbseq_window= 12
• nextflow_config - Config default value correct: params.mtbseq_distance= 12
• nextflow_config - Config default value correct: params.mtbseq_mincovr= 4
• nextflow_config - Config default value correct: params.mtbseq_user= root
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-tbanalyzer_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-tbanalyzer_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-tbanalyzer_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• actions_nf_test - '.github/workflows/nf-test.yml' is triggered on expected events
• actions_nf_test - '.github/workflows/nf-test.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 25.10.4, Config: 25.10.4
• readme - README nf-core template version badge found.
• pipeline_if_empty_null - No ifEmpty(null) strings found
• plugin_includes - No wrong validation plugin imports have been found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (0 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• system_exit - No System.exit calls found
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - assets/multiqc_config.yml found and not ignored.
• multiqc_config - assets/multiqc_config.yml contains report_section_order
• multiqc_config - assets/multiqc_config.yml contains export_plots
• multiqc_config - assets/multiqc_config.yml contains report_comment
• multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
• multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
• multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
• local_component_structure - local subworkflows directory structure is correct 'subworkflows/local/TOOL/SUBTOOL'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - TBBWA found in conf/modules.config and Nextflow scripts.
• modules_config - TBLIST found in conf/modules.config and Nextflow scripts.
• modules_config - TBVARIANTS found in conf/modules.config and Nextflow scripts.
• modules_config - TBFULL found in conf/modules.config and Nextflow scripts.
• modules_config - TBJOIN found in conf/modules.config and Nextflow scripts.
• modules_config - TBAMEND found in conf/modules.config and Nextflow scripts.
• modules_config - TBGROUPS found in conf/modules.config and Nextflow scripts.
• nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
• nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 4.0.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 4.0.2
• Run at 2026-06-24 21:30:21

[abhi18av]

Re-based the vendoring onto the pinned MAGMA v0.3.0 tag (f33a913, SciVer-validated 'Plan 1 complete') instead of the divergent feat/plan1-nfcore-modules tip.

• Source: mycobactopia-org/MAGMA branch tbanalyzer-v0.3.0 (v0.3.0 + magma_ namespacing + stub-def fixes).
• v0.3.0 splits into 16 subworkflows (adds call_wf/map_wf/merge_wf/quality_check_wf/reports_wf/structural_variants_analysis_wf/validate_fastqs_wf); re-vendored with sibling includes preserved.
• The GATK_MARK_DUPLICATES_DELLY arg-count bug (hand-fixed on feat/plan1) is absent in v0.3.0. Deferred trio (variantrecalibrator, snpsites, select_variants PHYLOGENY) is intentionally local — hermetic, no impact here.
• Next milestone to track: v0.4.0 (after Plan 3 Phase 4, MAGMA consumes the XBS subworkflow); SciVer surface expected to shift modestly (PLAN_3 §11.5).

Both modes parse (strict v2); full MAGMA DAG compiles under -stub-run. Biological Docker validation remains the deferred follow-up (draft until green).