github-actions[bot]
commented
3 weeks ago nf-core pipelines lint overall result: Passed :white_check_mark:
Posted for pipeline commit 6c6cd8c
+| ✅ 281 tests passed |+
### :white_check_mark: Tests passed:
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.gitattributes`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.gitignore`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.editorconfig`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.prettierignore`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `nextflow.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-taxprofiler_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/modules.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/test.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-taxprofiler_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-taxprofiler_logo_dark.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/output.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `docs/usage.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `main.nf`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `assets/multiqc_config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/base.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `conf/igenomes_ignored.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File found: `modules.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-taxprofiler_logo.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Utils.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowTaxprofiler.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `Singularity`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar`
* [files_exist](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Found nf-schema plugin
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.afterText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.command`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.summary.afterText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_time`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationFailUnrecognisedParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationLenientMode`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationSchemaIgnoreParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationShowHiddenParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` began with ``nf-core/``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>=
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``1.3.0dev``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.preprocessing_qc_tool= fastqc
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_qc_tool= fastp
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_qc_minlength= 15
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_tool= bbduk
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_adapterremoval_tool= porechop_abi
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_filter_tool= nanoq
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.longread_qc_qualityfilter_minquality= 7
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.shortread_redundancyestimation_mode= kmer
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.diamond_output_format= tsv
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.kaiju_taxon_rank= species
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.krakenuniq_batch_size= 20
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.malt_mode= BlastN
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ganon_report_type= reads
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ganon_report_rank= default
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ganon_report_toppercentile= 0
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ganon_report_mincount= 0
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ganon_report_maxcount= 0
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.standardisation_taxpasta_format= tsv
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.validate_params= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
* [nextflow_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nextflow_config) - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `CODE_OF_CONDUCT.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/CONTRIBUTING.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/config.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `assets/nf-core-taxprofiler_logo_light.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-taxprofiler_logo_light.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/images/nf-core-taxprofiler_logo_dark.png` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `docs/README.md` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template
* [actions_ci](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events
* [actions_ci](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version
* [actions_awstest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly
* [actions_awsfulltest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly
* [actions_awsfulltest](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test`
* [readme](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/readme) - README Nextflow minimum version badge matched config. Badge: `24.04.2`, Config: `24.04.2`
* [readme](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI.
* [pipeline_todos](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_todos) - No TODO strings found
* [plugin_includes](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/plugin_includes) - No wrong validation plugin imports have been found
* [pipeline_name_conventions](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention
* [template_strings](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/template_strings) - Did not find any Jinja template strings (0 files)
* [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Schema lint passed
* [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Schema title + description lint passed
* [schema_lint](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv'
* [schema_params](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config
* [system_exit](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/system_exit) - No `System.exit` calls found
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: template_version_comment.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml
* [merge_markers](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files
* [modules_json](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json`
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` found and not ignored.
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_section_order`
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `export_plots`
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_comment`
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` follows the ordering scheme of the minimally required plugins.
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains a matching 'report_comment'.
* [multiqc_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains 'export_plots: true'.
* [modules_structure](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `BRACKEN_BRACKEN` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `CENTRIFUGE_KREPORT` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `MEGAN_RMA2INFO_TSV` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `MEGAN_RMA2INFO_KRONA` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/base_config) - `FALCO` found in `conf/base.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `UNTAR` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FASTQC` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FASTQC_PROCESSED` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FALCO` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FALCO_PROCESSED` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FASTP_SINGLE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FASTP_PAIRED` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `ADAPTERREMOVAL_SINGLE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `ADAPTERREMOVAL_PAIRED` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `NONPAREIL_NONPAREIL` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `NONPAREIL_CURVE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `NONPAREIL_SET` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `NONPAREIL_NONPAREILCURVESR` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CAT_FASTQ` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PORECHOP_PORECHOP` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PORECHOP_ABI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `FILTLONG` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `NANOQ` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `BBMAP_BBDUK` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `PRINSEQPLUSPLUS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `BOWTIE2_BUILD` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `BOWTIE2_ALIGN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MINIMAP2_INDEX` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MINIMAP2_ALIGN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `SAMTOOLS_VIEW` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `SAMTOOLS_FASTQ` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `SAMTOOLS_STATS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MERGE_RUNS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MALT_RUN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MEGAN_RMA2INFO_TSV` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKEN2_KRAKEN2` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKEN2_STANDARD_REPORT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `BRACKEN_BRACKEN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `BRACKEN_COMBINEBRACKENOUTPUTS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKENTOOLS_COMBINEKREPORTS_KRAKEN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKENUNIQ_PRELOADEDKRAKENUNIQ` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKENTOOLS_KREPORT2KRONA` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRONA_CLEANUP` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRONA_KTIMPORTTEXT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MEGAN_RMA2INFO_KRONA` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRONA_KTIMPORTTAXONOMY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `METAPHLAN_METAPHLAN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `METAPHLAN_MERGEMETAPHLANTABLES` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CENTRIFUGE_CENTRIFUGE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `CENTRIFUGE_KREPORT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KAIJU_KAIJU` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KAIJU_KAIJU2TABLE_SINGLE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KAIJU_KAIJU2TABLE_COMBINED` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KAIJU_KAIJU2KRONA` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `DIAMOND_BLASTX` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MOTUS_PROFILE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MOTUS_MERGE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KMCP_SEARCH` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `KMCP_PROFILE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GANON_CLASSIFY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GANON_REPORT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `GANON_TABLE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `TAXPASTA_MERGE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `TAXPASTA_STANDARDISE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/modules_config) - `MULTIQC` found in `conf/modules.config` and Nextflow scripts.
* [nfcore_yml](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline`
* [nfcore_yml](https://nf-co.re/tools/docs/3.0.2/pipeline_lint_tests/nfcore_yml) - nf-core version in `.nf-core.yml` is set to the latest version: `3.0.2`
### Run details
* nf-core/tools version 3.0.2
* Run at `2024-10-31 10:26:34`
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).