Clean up code

[nbtm-sh]

• Removing hardcoded paths and adding sensible defaults

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit 9af55b1

+| ✅ 153 tests passed       |+
!| ❗  17 tests had warnings |!
-| ❌  52 tests failed       |-

❌ Test failures:

• schema_params - Param bfd_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param smallbfd_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param mgnify_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb70_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_mmcif_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param uniclust30_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param uniref90_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_seq_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param uniprot_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param alphafold_params_prefix from nextflow config not found in nextflow_schema.json
• schema_params - Param mmcif_path from nextflow config not found in nextflow_schema.json
• schema_params - Param mmcif_obsolete from nextflow config not found in nextflow_schema.json
• schema_params - Param uniclust30_db from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_first_non_consensus_sequences from nextflow config not found in nextflow_schema.json
• schema_params - Param uniprot_fasta from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_seqres_txt from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt from nextflow config not found in nextflow_schema.json
• schema_params - Param uniref90_fasta from nextflow config not found in nextflow_schema.json
• schema_params - Param mgy_clusters_fasta from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_name from nextflow config not found in nextflow_schema.json
• schema_params - Param smallbfd_name from nextflow config not found in nextflow_schema.json
• schema_params - Param mgnify_name from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb70_name from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_mmcif_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniclust30_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniref90_name from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_seqres_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniprot_name from nextflow config not found in nextflow_schema.json
• schema_params - Param alphafold_params_name from nextflow config not found in nextflow_schema.json
• schema_params - Param mmcif_files_name from nextflow config not found in nextflow_schema.json
• schema_params - Param mmcif_obsolete_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniclust30_db_name from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_first_non_consensus_sequences_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniprot_fasta_name from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_seqres_txt_name from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_metaclust_clu_complete_id30_c90_final_seq_sorted_opt_name from nextflow config not found in nextflow_schema.json
• schema_params - Param uniref90_fasta_name from nextflow config not found in nextflow_schema.json
• schema_params - Param mgy_clusters_fasta_name from nextflow config not found in nextflow_schema.json
• schema_params - Param cpuQueue from nextflow config not found in nextflow_schema.json
• schema_params - Param gpuQueue from nextflow config not found in nextflow_schema.json
• schema_params - Param bfd_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param small_bfd_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param mgnify_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb70_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_mmcif_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param uniclust30_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param uniref90_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param pdb_seqres_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param uniprot_dir_path from nextflow config not found in nextflow_schema.json
• schema_params - Param mgnify_database_path from nextflow config not found in nextflow_schema.json
• schema_params - Param template_mmcif_dir from nextflow config not found in nextflow_schema.json
• schema_params - Param obsolete_pdbs_path from nextflow config not found in nextflow_schema.json

❗ Test warnings:

• files_exist - File not found: conf/igenomes.config
• files_exist - File not found: lib/WorkflowProteinfold.groovy
• nextflow_config - Config manifest.version should end in dev: '1.0.0'
• pipeline_todos - TODO string in README.md: Write a 1-2 sentence summary of what data the pipeline is for and what it does
• pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
• pipeline_todos - 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 - TODO string in README.md: Add bibliography of tools and data used in your pipeline
• pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
• pipeline_todos - TODO string in katana.config: Check the defaults for all processes
• pipeline_todos - TODO string in katana.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in base.config: Check the defaults for all processes
• pipeline_todos - TODO string in base.config: Customise requirements for specific processes.
• pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
• pipeline_todos - TODO string in check_samplesheet.py: Update the script to check the samplesheet
• pipeline_todos - TODO string in check_samplesheet.py: Update the check_samplesheet function
• pipeline_todos - TODO string in check_samplesheet.py: Update the column names for the input samplesheet
• pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release

✅ Tests passed:

• files_exist - File found: .gitattributes
• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .editorconfig
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: CODE_OF_CONDUCT.md
• files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
• files_exist - File found: nextflow_schema.json
• files_exist - File found: nextflow.config
• files_exist - File found: README.md
• files_exist - File found: .github/.dockstore.yml
• files_exist - File found: .github/CONTRIBUTING.md
• files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• files_exist - File found: .github/workflows/branch.yml
• files_exist - File found: .github/workflows/ci.yml
• files_exist - File found: .github/workflows/linting_comment.yml
• files_exist - File found: .github/workflows/linting.yml
• files_exist - File found: assets/email_template.html
• files_exist - File found: assets/email_template.txt
• files_exist - File found: assets/sendmail_template.txt
• files_exist - File found: assets/nf-core-proteinfold_logo_light.png
• files_exist - File found: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: docs/images/nf-core-proteinfold_logo_light.png
• files_exist - File found: docs/images/nf-core-proteinfold_logo_dark.png
• files_exist - File found: docs/output.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/README.md
• files_exist - File found: docs/usage.md
• files_exist - File found: lib/nfcore_external_java_deps.jar
• files_exist - File found: lib/NfcoreSchema.groovy
• files_exist - File found: lib/NfcoreTemplate.groovy
• files_exist - File found: lib/Utils.groovy
• files_exist - File found: lib/WorkflowMain.groovy
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: .github/workflows/awstest.yml
• files_exist - File found: .github/workflows/awsfulltest.yml
• files_exist - File found: modules.json
• files_exist - File found: pyproject.toml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: .nf-core.yaml
• files_exist - File not found check: bin/markdown_to_html.r
• files_exist - File not found check: conf/aws.config
• files_exist - File not found check: .github/workflows/push_dockerhub.yml
• files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: docs/images/nf-core-proteinfold_logo.png
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: .travis.yml
• nextflow_config - Config variable found: manifest.name
• nextflow_config - Config variable found: manifest.nextflowVersion
• nextflow_config - Config variable found: manifest.description
• nextflow_config - Config variable found: manifest.version
• nextflow_config - Config variable found: manifest.homePage
• nextflow_config - Config variable found: timeline.enabled
• nextflow_config - Config variable found: trace.enabled
• nextflow_config - Config variable found: report.enabled
• nextflow_config - Config variable found: dag.enabled
• nextflow_config - Config variable found: process.cpus
• nextflow_config - Config variable found: process.memory
• nextflow_config - Config variable found: process.time
• nextflow_config - Config variable found: params.outdir
• nextflow_config - Config variable found: params.input
• nextflow_config - Config variable found: params.show_hidden_params
• nextflow_config - Config variable found: params.schema_ignore_params
• nextflow_config - Config variable found: manifest.mainScript
• nextflow_config - Config variable found: timeline.file
• nextflow_config - Config variable found: trace.file
• nextflow_config - Config variable found: report.file
• nextflow_config - Config variable found: dag.file
• nextflow_config - Config variable (correctly) not found: params.nf_required_version
• nextflow_config - Config variable (correctly) not found: params.container
• nextflow_config - Config variable (correctly) not found: params.singleEnd
• nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
• nextflow_config - Config variable (correctly) not found: params.name
• nextflow_config - Config variable (correctly) not found: params.enable_conda
• nextflow_config - Config timeline.enabled had correct value: true
• nextflow_config - Config report.enabled had correct value: true
• nextflow_config - Config trace.enabled had correct value: true
• nextflow_config - Config dag.enabled had correct value: true
• nextflow_config - Config manifest.name began with nf-core/
• nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
• nextflow_config - Config dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config params.custom_config_version is set to master
• nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
• nextflow_config - Lines for loading custom profiles found
• files_unchanged - .gitattributes matches the template
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - CODE_OF_CONDUCT.md matches the template
• files_unchanged - LICENSE matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/CONTRIBUTING.md matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
• files_unchanged - .github/workflows/branch.yml matches the template
• files_unchanged - .github/workflows/linting_comment.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - assets/email_template.html matches the template
• files_unchanged - assets/email_template.txt matches the template
• files_unchanged - assets/sendmail_template.txt matches the template
• files_unchanged - assets/nf-core-proteinfold_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-proteinfold_logo_light.png matches the template
• files_unchanged - docs/images/nf-core-proteinfold_logo_dark.png matches the template
• files_unchanged - docs/README.md matches the template
• files_unchanged - lib/nfcore_external_java_deps.jar matches the template
• files_unchanged - lib/NfcoreSchema.groovy matches the template
• files_unchanged - lib/NfcoreTemplate.groovy matches the template
• files_unchanged - .gitignore matches the template
• files_unchanged - .prettierignore matches the template
• files_unchanged - pyproject.toml matches the template
• actions_ci - '.github/workflows/ci.yml' is triggered on expected events
• actions_ci - '.github/workflows/ci.yml' checks minimum NF version
• actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
• actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• readme - README Nextflow minimum version in Quick Start section matched config. README: 22.10.1, Config: 22.10.1
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (141 files)
• schema_lint - Schema lint passed
• schema_lint - Schema title + description lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: branch.yml
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins.
• multiqc_config - 'assets/multiqc_config.yml' contains a matching 'report_comment'.
• multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

• nf-core/tools version 2.7.2
• Run at 2024-10-10 01:28:46