DSL2: Nf test conversion: shortDNA

[merszym]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/eager/tree/master/.github/CONTRIBUTING.md)
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

This is the PR for Issue #1135

[github-actions]

nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 36c3da1

+| ✅ 267 tests passed       |+
#| ❔   2 tests were ignored |#
#| ❔   1 tests had warnings |#
!| ❗  45 tests had warnings |!

Details

❗ Test warnings:

• pipeline_todos - TODO string in nextflow.config: Specify your pipeline's command line flags
• 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 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 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 awsfulltest.yml: You can customise AWS full pipeline tests as required
• 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!
• 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 nextflow.config: Specify any additional parameters here
• 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 - 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 - reference_indexing.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 - merge_lanes_inputbam.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 - preprocessing_fastp.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 - elongate_reference.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 - preprocessing_adapterremoval.nf in subworkflows/local should be moved to a SUBWORKFLOW_NAME/main.nf structure
• local_component_structure - deduplicate.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 - circularmapper.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 - preprocessing.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 - reference_indexing_multi.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 - reference_indexing_single.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 - run_sex_determination.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

❔ Tests ignored:

• nextflow_config - nextflow_config
• schema_params - schema_params

❔ Tests fixed:

• rocrate_readme_sync - Mismatch fixed: RO-Crate description updated from README.md.

✅ 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/default.nf.test' contains outdir parameter
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/default.nf.test' snapshots a 'versions.yml' file
• 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_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_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/test_microbial.nf.test' snapshots a 'versions.yml' file
• nf_test_content - 'tests/shortdna.nf.test' contains outdir parameter
• nf_test_content - 'tests/shortdna.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: 25.10.2, Config: 25.10.2
• 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.yml
• actions_schema_validation - Workflow validation passed: download_pipeline.yml
• actions_schema_validation - Workflow validation passed: template-version-comment.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: release-announcements.yml
• actions_schema_validation - Workflow validation passed: fix_linting.yml
• actions_schema_validation - Workflow validation passed: nf-test.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: clean-up.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: 3.5.1
• rocrate_readme_sync - RO-Crate description matches the README.md.

Run details

• nf-core/tools version 3.5.1
• Run at 2026-01-30 10:09:59

[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.

[TCLamnidis]

Metagenomics section still needs tweaking, but the rest seems consistent. Try again on a different day to ensure no timestamps are used also.

[merszym]

Tests are done, double check on another day required

[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)
• Rename test to match new naming scheme
• exclude preseq command log from md5sum checks

[merszym]

Todo: test on another day to catch timestamps

[merszym]

Tested one week later (forgot to commit final changes last week) - all tests passed

[merszym]

TODO:

• Merge with dev once template-3.4.1 is merged with dev

[merszym]

@TCLamnidis This PR should now be ready for merge :)