Fixed S3 bucket path in conditional statements

[nschcolnicov]

Fixed the issue reported here: https://github.com/nf-core/rnavar/issues/121 It was a simple fix, the conditional statement wasn't working because it was missing a "/" to match the one defined in the nextflow.config, so the snpEff cache data dir wasn't being built properly.

To test it I ran the command: nextflow run ../../main.nf -profile test,docker --annotate_tools snpeff --outdir . -resume --download_cache

@maxulysse There are two more issues that I spotted that the publishDir for snpEff and VEP contain a null value, I will create an issue for this address it on a separate PR

PR checklist

• [x] This comment contains a description of changes (with reason).
• [x] If you've fixed a bug or added code that should be tested, add tests!
  • [x] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [x] If necessary, also make a PR on the nf-core/rnavar branch on the nf-core/test-datasets repository.
• [x] Make sure your code lints (nf-core lint).
• [x] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [x] Usage Documentation in docs/usage.md is updated.
• [x] Output Documentation in docs/output.md is updated.
• [x] CHANGELOG.md is updated.
• [x] README.md is updated (including new tool citations and authors/contributors).

[github-actions[bot]]

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

Posted for pipeline commit a42bb7e

+| ✅ 188 tests passed       |+
!| ❗   4 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [pipeline_todos](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `README.md`: _Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets._ * [pipeline_todos](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `awsfulltest.yml`: _You can customise AWS full pipeline tests as required_ * [pipeline_todos](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `WorkflowRnavar.groovy`: _Optionally add in-text citation tools to this list._ * [pipeline_todos](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _#Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline_ ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_exist.html) - 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Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``manifest.name`` began with ``nf-core/`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable ``manifest.homePage`` began with https://github.com/nf-core/ * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config ``manifest.version`` ends in ``dev``: ``1.1.0dev`` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_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/2.12.1/pipeline_lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - nextflow.config contains configuration profile `test` * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.read_length= 150.0 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/ * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.aligner= star * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.star_max_memory_bamsort= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.star_bins_bamsort= 50 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.star_max_collapsed_junc= 1000000 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.seq_platform= illumina * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_hc_call_conf= 20.0 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/ * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/ * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.vep_out_format= vcf * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_interval_scatter_count= 25 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_vf_window_size= 35 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_vf_cluster_size= 3 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_vf_fs_filter= 30.0 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.gatk_vf_qd_filter= 2.0 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.custom_config_version= master * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.max_cpus= 16 * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.max_memory= 128.GB * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.max_time= 240.h * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.publish_dir_mode= copy * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.max_multiqc_email_size= 25.MB * [nextflow_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/nextflow_config.html) - Config default value correct: params.validate_params= true * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `CODE_OF_CONDUCT.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/CONTRIBUTING.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/bug_report.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/config.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.github/workflows/linting.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `assets/sendmail_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `assets/nf-core-rnavar_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-rnavar_logo_light.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `docs/images/nf-core-rnavar_logo_dark.png` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `lib/NfcoreTemplate.groovy` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `.prettierignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/files_unchanged.html) - `pyproject.toml` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [actions_awstest](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_awstest.html) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_awsfulltest.html) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `23.04.0`, Config: `23.04.0` * [readme](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/template_strings.html) - Did not find any Jinja template strings (309 files) * [schema_lint](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/csv' * [schema_params](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [system_exit](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/system_exit.html) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: release-announcements.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: download_pipeline.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/actions_schema_validation.html) - Workflow validation passed: awsfulltest.yml * [merge_markers](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.12.1/pipeline_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/2.12.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains a matching 'report_comment'. * [multiqc_config](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.12.1/pipeline_lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.12.1 * Run at `2024-02-12 09:33:15`

[maxulysse]

@nf-core-bot fix linting pretty please