DSL2: Add nf-test microbial

[TCLamnidis]

Linked to #1138

nf-test conversion for test_microbial

Still need to check that all files are picked up by snapshots, this is just the initial setup, using the test profile as a guide.

[nf-core-bot]

Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.2.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 824f340

+| ✅ 261 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗  45 tests had warnings |!

Details

❗ Test warnings:

• 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
• pipeline_todos - TODO string in main.nf: Remove this line if you don't need a FASTA file
• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• 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 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 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 test_minimal.config: Specify the paths to your test data on nf-core/test-datasets
• pipeline_todos - TODO string in test_minimal.config: Give any required params for the test so that command line flags are not needed
• pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
• pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here
• 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 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!
• local_component_structure - build_intervals.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - print_contamination_angsd.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - filter_bam_fragment_length.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - collect_genotypes.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - samtools_view_genome.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - host_removal.nf in modules/local should be moved to a TOOL/SUBTOOL/main.nf structure
• local_component_structure - deduplicate.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - merge_lanes_inputbam.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - reference_indexing_single.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - map.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - manipulate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - reference_indexing_multi.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - metagenomics_complexityfilter.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - bamfiltering.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - estimate_contamination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - run_sex_determination.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - metagenomics_postprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - preprocessing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - preprocessing_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - calculate_damage.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - merge_libraries.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - metagenomics.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - genotype.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - reference_indexing.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - preprocessing_fastp.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - circularmapper.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - metagenomics_profiling.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - elongate_reference.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure

❔ Tests ignored:

• nextflow_config - nextflow_config
• schema_params - schema_params

✅ 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/CONTRIBUTING.md
• 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-eager_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/images/nf-core-eager_logo_light.png
• files_exist - File found: docs/images/nf-core-eager_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-eager_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/WorkflowEager.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
• nf_test_content - 'tests/test_humanpopgen.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_humanpopgen.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_minimal.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_minimal.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/test_microbial.nf.test' contains outdir parameter
• nf_test_content - 'tests/test_microbial.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/nextflow.config' contains modules_testdata_base_path
• nf_test_content - 'tests/nextflow.config' contains pipelines_testdata_base_path
• nf_test_content - 'nf-test.config' sets a testsDir
• nf_test_content - 'nf-test.config' sets a workDir
• nf_test_content - 'nf-test.config' sets a configFile
• 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/CONTRIBUTING.md 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-eager_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-eager_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-eager_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: 24.10.5, Config: 24.10.5
• readme - README nf-core template version badge found.
• readme - README Zenodo placeholder was replaced with DOI.
• 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: linting_comment.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: clean-up.yml
• actions_schema_validation - Workflow validation passed: nf-test.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'
• base_config - conf/base.config found and not ignored.
• modules_config - conf/modules.config found and not ignored.
• modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_CONVERT_BAM_INPUT found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ_CONVERTED_BAM found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
• modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - FALCO found in conf/modules.config and Nextflow scripts.
• modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
• modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
• modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
• modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ_ADAPTERREMOVAL found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_PMDFASTA found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FAIDX found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_CREATESEQUENCEDICTIONARY found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - GUNZIP_ELONGATED_FASTA found in conf/modules.config and Nextflow scripts.
• modules_config - CIRCULARMAPPER_CIRCULARGENERATOR found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_INDEX_CIRCULARISED found in conf/modules.config and Nextflow scripts.
• modules_config - MAPAD_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_BAM_INPUT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_MERGE_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES_BAMINPUT found in conf/modules.config and Nextflow scripts.
• modules_config - FILTER_BAM_FRAGMENT_LENGTH found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_VIEW_BAM_FILTERING found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_LENGTH_FILTER_INDEX found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT_FILTERED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FASTQ_SAVEBAMFILTERINGREADS found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FASTQ_METAGENOMICS found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_FASTQ_METAGENOMICS found in conf/modules.config and Nextflow scripts.
• modules_config - SEQKIT_SPLIT2 found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_ALN found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_SAMSE found in conf/modules.config and Nextflow scripts.
• modules_config - BWA_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - MAPAD_MAP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT_MAPAD found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_MEM found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_MERGE_LANES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_MERGED_LANES found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT_MERGED_LANES found in conf/modules.config and Nextflow scripts.
• modules_config - CIRCULARMAPPER_REALIGNSAMFILE found in conf/modules.config and Nextflow scripts.
• modules_config - PICARD_MARKDUPLICATES found in conf/modules.config and Nextflow scripts.
• modules_config - DEDUP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_MERGE_DEDUPPED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_SORT_DEDUPPED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_DEDUPPED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT_DEDUPPED found in conf/modules.config and Nextflow scripts.
• modules_config - HOST_REMOVAL found in conf/modules.config and Nextflow scripts.
• modules_config - ENDORSPY found in conf/modules.config and Nextflow scripts.
• modules_config - PRESEQ_CCURVE found in conf/modules.config and Nextflow scripts.
• modules_config - PRESEQ_LCEXTRAP found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_VIEW_GENOME found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_COVERAGE_DEPTH found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_COVERAGE_BREADTH found in conf/modules.config and Nextflow scripts.
• modules_config - ANGSD_DOCOUNTS found in conf/modules.config and Nextflow scripts.
• modules_config - ANGSD_CONTAMINATION found in conf/modules.config and Nextflow scripts.
• modules_config - PRINT_CONTAMINATION_ANGSD found in conf/modules.config and Nextflow scripts.
• modules_config - MTNUCRATIO found in conf/modules.config and Nextflow scripts.
• modules_config - QUALIMAP_BAMQC_WITHBED found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
• modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
• modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
• modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
• modules_config - AMPS found in conf/modules.config and Nextflow scripts.
• modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
• modules_config - DAMAGEPROFILER found in conf/modules.config and Nextflow scripts.
• modules_config - CALCULATE_MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_DEPTH_SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
• modules_config - SEXDETERRMINE found in conf/modules.config and Nextflow scripts.
• modules_config - BEDTOOLS_MASKFASTA found in conf/modules.config and Nextflow scripts.
• modules_config - MAPDAMAGE2 found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_DAMAGE_RESCALED found in conf/modules.config and Nextflow scripts.
• modules_config - PMDTOOLS_FILTER found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_FLAGSTAT_DAMAGE_FILTERED found in conf/modules.config and Nextflow scripts.
• modules_config - BAMUTIL_TRIMBAM found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_INDEX_DAMAGE_TRIMMED found in conf/modules.config and Nextflow scripts.
• modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
• modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
• modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
• modules_config - CAT_CAT_MALT found in conf/modules.config and Nextflow scripts.
• modules_config - UNTAR_METAGENOMICS found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
• modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
• modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
• modules_config - MALTEXTRACT found in conf/modules.config and Nextflow scripts.
• modules_config - MEGAN_RMA2INFO found in conf/modules.config and Nextflow scripts.
• modules_config - AMPS found in conf/modules.config and Nextflow scripts.
• modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
• modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
• modules_config - SAMTOOLS_MPILEUP_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
• modules_config - SEQUENCETOOLS_PILEUPCALLER found in conf/modules.config and Nextflow scripts.
• modules_config - COLLECT_GENOTYPES found in conf/modules.config and Nextflow scripts.
• modules_config - EIGENSTRATDATABASETOOLS_EIGENSTRATSNPCOVERAGE found in conf/modules.config and Nextflow scripts.
• modules_config - GATK_REALIGNERTARGETCREATOR found in conf/modules.config and Nextflow scripts.
• modules_config - GATK_INDELREALIGNER found in conf/modules.config and Nextflow scripts.
• modules_config - GATK_UNIFIEDGENOTYPER found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_INDEX_UG found in conf/modules.config and Nextflow scripts.
• modules_config - GATK4_HAPLOTYPECALLER found in conf/modules.config and Nextflow scripts.
• modules_config - FREEBAYES found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_INDEX_FREEBAYES found in conf/modules.config and Nextflow scripts.
• modules_config - BCFTOOLS_STATS_GENOTYPING found in conf/modules.config and Nextflow scripts.
• modules_config - ANGSD_GL 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: 3.3.2
• rocrate_readme_sync - RO-Crate descriptions are in sync with README.md.

Run details

• nf-core/tools version 3.3.2
• Run at 2025-09-16 11:28:03

[TCLamnidis]

Qualimap results for hs37d5 are missing. This is because there is no overlap with the 1240K SNPs in the file? It looks like when it gets to the qualimap process, the BAM only contains 16 reads...
A report is still generated, but the raw data and figures outputs are not there.

[TCLamnidis]

Checked, and all files in the all_files are tested again properly in the specific subsections

[merszym]

Test passed :)

[TCLamnidis]

ToDos:

• merge latest changes from dev (includes new nf-core template)
• Add profile tag to the test so it works with the new CI runner
• Update commands in the instructions for how to update the test in future
• Update snapshots to work with latest template (MultiQC got a version bump)

[TCLamnidis]

Woohoo! 🎉