github-actions[bot]
commented
1 month ago nf-core pipelines lint overall result: Passed :white_check_mark: :warning:
Posted for pipeline commit d7f6715
+| ✅ 201 tests passed |+
#| ❔ 30 tests were ignored |#
!| ❗ 1 tests had warnings |!
### :heavy_exclamation_mark: Test warnings:
* [schema_lint](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/schema_lint) - Schema `$id` should be `https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/master/nextflow_schema.json`
Found `https://raw.githubusercontent.com/plant-food-research-open/assemblyqc/main/nextflow_schema.json`
### :grey_question: Tests ignored:
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `conf/igenomes.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `conf/igenomes_ignored.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `assets/multiqc_config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `CODE_OF_CONDUCT.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `assets/nf-core-assemblyqc_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `docs/images/nf-core-assemblyqc_logo_light.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `docs/images/nf-core-assemblyqc_logo_dark.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `.github/ISSUE_TEMPLATE/config.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `.github/workflows/awstest.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File is ignored: `.github/workflows/awsfulltest.yml`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `manifest.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `manifest.homePage`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `validation.help.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `validation.help.afterText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `validation.summary.beforeText`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ignored: `validation.summary.afterText`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File does not exist: `CODE_OF_CONDUCT.md`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/CONTRIBUTING.md`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File does not exist: `.github/ISSUE_TEMPLATE/config.yml`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/PULL_REQUEST_TEMPLATE.md`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/workflows/branch.yml`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `.github/workflows/linting.yml`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File does not exist: `assets/nf-core-assemblyqc_logo_light.png`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File does not exist: `docs/images/nf-core-assemblyqc_logo_light.png`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File does not exist: `docs/images/nf-core-assemblyqc_logo_dark.png`
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - File ignored due to lint config: `docs/README.md`
* [actions_awstest](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_awstest) - 'awstest.yml' workflow not found: `/home/runner/work/assemblyqc/assemblyqc/.github/workflows/awstest.yml`
* [template_strings](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/template_strings) - template_strings
* [multiqc_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/multiqc_config) - multiqc_config
### :white_check_mark: Tests passed:
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.gitattributes`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.gitignore`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.editorconfig`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.prettierignore`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `nextflow.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `conf/modules.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `conf/test.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `docs/output.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `docs/README.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `docs/usage.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `main.nf`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `conf/base.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File found: `modules.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-assemblyqc_logo.png`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Utils.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowAssemblyqc.groovy`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `Singularity`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar`
* [files_exist](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Found nf-schema plugin
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.enabled`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable found: `validation.help.command`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_cpus`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_memory`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.max_time`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationFailUnrecognisedParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationLenientMode`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationSchemaIgnoreParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.validationShowHiddenParams`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>=
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``2.2.0+dev``
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/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/3.0.1/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test`
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.check_sequence_duplicates= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.assemblathon_stats_n_limit= 100
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.gfastats_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ncbi_fcs_adaptor_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.ncbi_fcs_gx_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.contamination_stops_pipeline= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.busco_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.tidk_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.tidk_filter_size_bp= 1000000
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.lai_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.kraken2_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.hic_fastp_ext_args= --qualified_quality_phred 20 --length_required 50
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_mummer_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_plotsr_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_between_input_assemblies= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_mummer_plot_type= both
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_mummer_max_gap= 1000000
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_mummer_min_bundle_size= 1000000
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_color_by_contig= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.synteny_plotsr_seq_label= Chr
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.merqury_skip= true
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.merqury_kmer_length= 21
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master
* [nextflow_config](https://nf-co.re/tools/docs/3.0.1/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/3.0.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template
* [files_unchanged](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template
* [actions_ci](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events
* [actions_ci](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' checks minimum NF version
* [readme](https://nf-co.re/tools/docs/3.0.1/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/3.0.1/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI.
* [pipeline_todos](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/pipeline_todos) - No TODO strings found
* [plugin_includes](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/plugin_includes) - No wrong validation plugin imports have been found
* [pipeline_name_conventions](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention
* [schema_lint](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/schema_lint) - Schema lint passed
* [schema_lint](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv'
* [schema_params](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/schema_params) - Schema matched params returned from nextflow config
* [system_exit](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/system_exit) - No `System.exit` calls found
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml
* [actions_schema_validation](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml
* [merge_markers](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files
* [modules_json](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json`
* [modules_structure](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `NCBI_FCS_GX_SCREEN_SAMPLES` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `KRAKEN2` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `BWA_MEM` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `SAMBLASTER` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `DNADIFF` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `MERQURY_HAPMERS` found in `conf/base.config` and Nextflow scripts.
* [base_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/base_config) - `CREATEREPORT` found in `conf/base.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `SEQKIT_RMDUP` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `ASSEMBLATHON_STATS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `GFASTATS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `FCS_FCSADAPTOR` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `NCBI_FCS_GX_SCREEN_SAMPLES` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `NCBI_FCS_GX_KRONA_PLOT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `KRAKEN2` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `KRAKEN2_KRONA_PLOT` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `CIRCOS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `LINEARSYNTENY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `MINIMAP2_ALIGN` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `FILTER_BY_LENGTH` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `SORT_BY_LENGTH` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TIDK_EXPLORE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TIDK_SEARCH_APRIORI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TIDK_SEARCH_APOSTERIORI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TIDK_PLOT_APRIORI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TIDK_PLOT_APOSTERIORI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `CUSTOM_SHORTENFASTAIDS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `LTRHARVEST` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `LTRFINDER` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `LTRRETRIEVER_LTRRETRIEVER` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `CUSTOM_RESTOREGFFIDS` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `LTRRETRIEVER_LAI` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `BWA_MEM` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `SAMBLASTER` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `AGP2ASSEMBLY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `ASSEMBLY2BEDPE` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `HIC2HTML` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `HICQC` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `RUNASSEMBLYVISUALIZER` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `TAG_ASSEMBLY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `MERQURY_MERQURY` found in `conf/modules.config` and Nextflow scripts.
* [modules_config](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/modules_config) - `CREATEREPORT` found in `conf/modules.config` and Nextflow scripts.
* [nfcore_yml](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline`
* [nfcore_yml](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/nfcore_yml) - nf-core version in `.nf-core.yml` is set to the latest version: `3.0.1`
### Run details
* nf-core/tools version 3.0.1
* Run at `2024-10-09 23:59:19`
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).