Now using nf-test for pipeline level testing

`nf-core pipelines lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit a03629a

+| ✅ 165 tests passed       |+
#| ❔  31 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_ci](https://nf-co.re/tools/docs/3.0.1/pipeline_lint_tests/actions_ci) - actions_ci * [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 * [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. * [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 `2024-10-10 08:37:47`

Plant-Food-Research-Open / assemblyqc