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Australian-Structural-Biology-Computing / proteinfold

Protein 3D structure prediction pipeline
https://nf-co.re/proteinfold
MIT License
3 stars 0 forks source link

Clean up code #9

Closed nbtm-sh closed 1 day ago

nbtm-sh commented 2 months ago
github-actions[bot] commented 1 day ago

nf-core lint overall result: Failed :x:

Posted for pipeline commit 9af55b1

+| ✅ 153 tests passed       |+
!| ❗  17 tests had warnings |!
-| ❌  52 tests failed       |-
### :x: Test failures: * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `smallbfd_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgnify_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb70_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_mmcif_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniclust30_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniref90_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_seq_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniprot_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `alphafold_params_prefix` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mmcif_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mmcif_obsolete` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniclust30_db` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_first_non_consensus_sequences` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniprot_fasta` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_seqres_txt` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniref90_fasta` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgy_clusters_fasta` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `smallbfd_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgnify_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb70_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_mmcif_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniclust30_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniref90_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_seqres_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniprot_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `alphafold_params_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mmcif_files_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mmcif_obsolete_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniclust30_db_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_first_non_consensus_sequences_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniprot_fasta_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_seqres_txt_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniref90_fasta_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgy_clusters_fasta_name` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `cpuQueue` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `gpuQueue` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `bfd_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `small_bfd_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgnify_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb70_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_mmcif_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniclust30_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniref90_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `pdb_seqres_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `uniprot_dir_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `mgnify_database_path` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `template_mmcif_dir` from `nextflow config` not found in nextflow_schema.json * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Param `obsolete_pdbs_path` from `nextflow config` not found in nextflow_schema.json ### :heavy_exclamation_mark: Test warnings: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found: `lib/WorkflowProteinfold.groovy` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.0.0'`` * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Write a 1-2 sentence summary of what data the pipeline is for and what it does_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Add full-sized test dataset and amend the paragraph below if applicable_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Add bibliography of tools and data used in your pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `usage.md`: _Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `katana.config`: _Check the defaults for all processes_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `katana.config`: _Customise requirements for specific processes._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Check the defaults for all processes_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `base.config`: _Customise requirements for specific processes._ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `check_samplesheet.py`: _Update the script to check the samplesheet_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `check_samplesheet.py`: _Update the check_samplesheet function_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `check_samplesheet.py`: _Update the column names for the input samplesheet_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `WorkflowMain.groovy`: _Add Zenodo DOI for pipeline after first release_ ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/nf-core-proteinfold_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-proteinfold_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/images/nf-core-proteinfold_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `modules.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `pyproject.toml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `docs/images/nf-core-proteinfold_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/nf-core-proteinfold_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-proteinfold_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/images/nf-core-proteinfold_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools-docs/lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `22.10.1`, Config: `22.10.1` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version in Quick Start section matched config. README: `22.10.1`, Config: `22.10.1` * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (141 files) * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.7.2 * Run at `2024-10-10 01:28:46`