add customized multiqc config file

[azmigueldario]

PR checklist

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

Added reports for all multiqc-supported tools. The software versions should be automatically updated.

[github-actions[bot]]

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks. To fix this CI test, please run:

• Install black: pip install black
• Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment :+1:

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

[github-actions[bot]]

nf-core lint overall result: Failed :x:

Posted for pipeline commit 10f4c27

+| ✅ 234 tests passed       |+
!| ❗  83 tests had warnings |!
-| ❌  87 tests failed       |-

### :x: Test failures: * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File must be removed: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/nfcore_external_java_deps.jar` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable not found: `params.validationShowHiddenParams` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable not found: `params.validationSchemaIgnoreParams` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``manifest.name`` did not begin with ``nf-core/``: cidgoh/bacpaq * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.homePage`` did not begin with https://github.com/nf-core/: https://github.com/cidgoh/bacpaq * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.mode` is set as `illumina` in `nextflow_schema.json` but is `nanopore` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.adapter_fasta` is set as `https://object-arbutus.cloud.computecanada.ca/cidgohshare/database/adaptors/test.fa` in `nextflow_schema.json` but is `/mnt/cidgoh-object-storage/database/adaptors/test.fa` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.skip_subsampling` is set as `true` in `nextflow_schema.json` but is `false` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.save_merged` is set as `true` in `nextflow_schema.json` but is `false` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.depth_cut_off` is set as `50,80` in `nextflow_schema.json` but is `50` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Default value from the Nextflow schema `params.tracedir = `25.MB`` not found in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.validate_params` is set as `true` in `nextflow_schema.json` but is `false` in `nextflow.config`. * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value incorrect: `params.schema_ignore_params` is set as `fasta` in `nextflow_schema.json` but is `genomes` in `nextflow.config`. * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/CONTRIBUTING.md` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/bug_report.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/ISSUE_TEMPLATE/feature_request.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/PULL_REQUEST_TEMPLATE.md` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/workflows/branch.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting_comment.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/workflows/linting.yml` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `assets/email_template.html` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `assets/email_template.txt` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `assets/sendmail_template.txt` does not match the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `docs/README.md` does not match the template * [actions_ci](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci) - Minimum pipeline NF version '22.01.0' is not tested in '.github/workflows/ci.yml' * [readme](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/readme) - README Nextflow minimum version badge does not match config. Badge: `23.04.0`, Config: `22.01.0` * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/modules/local/RMLST/ubuntu_curl_test.sif` L319578: b{{XmwçDçË{«=4‘¼Ö¶?fÍÛpÕ}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-angular.mjs` L2: "{{","}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-angular.mjs` L2: "{{",I="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{{",e.strip.open&&(this.buffer+="~"),this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.strip.close&&(this.buffer+="~"),this.buffer+=e.escaped?"}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{#",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.program.blockParams.length&&this.BlockParams(e.program.blockParams),e.chained?this.buffer+=e.inverseStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{",this.buffer+="else",this.buffer+=e.inverseStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{/",this.Expression(e.path),this.buffer+=e.closeStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{>",this.Expression(e.name),this.Params(e.params),this.Hash(e.hash),this.buffer+="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L6: "{{",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),this.buffer+="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{ "+this.SubExpression(l)+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{ DIRECTIVE "+this.SubExpression(l)+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{^}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{> "+e+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{> "+e+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L12: "{{! '"+l.value+"' }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L26: `{{${(0,c.printLiteral)(b)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L27: ({{> ...}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L27: `{{#${M.path}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs` L27: `{{#${C.path}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-html.mjs` L34: "{{","}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-html.mjs` L35: "{{ '{' }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-markdown.mjs` L75: |{{.*?}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs` L75: "{{",Re(H,X),"}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs` L107: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs` L110: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs` L110: "{{",d(Z),"}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js` L32245: "{{", printPathAndParams(path, print2), "}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js` L35748: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js` L36588: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js` L36602: "{{", replaceTextEndOfLine(part), "}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-angular.js` L2: "{{","}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-angular.js` L2: "{{",I="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{{",e.strip.open&&(this.buffer+="~"),this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.strip.close&&(this.buffer+="~"),this.buffer+=e.escaped?"}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{#",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),e.program.blockParams.length&&this.BlockParams(e.program.blockParams),e.chained?this.buffer+=e.inverseStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{",this.buffer+="else",this.buffer+=e.inverseStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{/",this.Expression(e.path),this.buffer+=e.closeStrip.close?"~}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{>",this.Expression(e.name),this.Params(e.params),this.Hash(e.hash),this.buffer+="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L6: "{{",this.Expression(e.path),this.Params(e.params),this.Hash(e.hash),this.buffer+="}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{ "+this.SubExpression(o)+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{ DIRECTIVE "+this.SubExpression(o)+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{^}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{> "+e+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{> "+e+" }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L12: "{{! '"+o.value+"' }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L26: `{{${(0,c.printLiteral)(b)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L27: ({{> ...}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L27: `{{#${M.path}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js` L27: `{{#${C.path}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-html.js` L34: "{{","}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-html.js` L35: "{{ '{' }} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-markdown.js` L75: |{{.*?}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js` L75: "{{",Re(H,X),"}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js` L107: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js` L110: /{{(.+?)}} * [template_strings](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/template_strings) - Found a Jinja template string in `/home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js` L110: "{{",y(Z),"}} * [schema_params](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_params) - Default value for param `skip_subsampling` invalid: Schema default (`True`) does not match the config default (`false`) * [schema_params](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_params) - Default value for param `save_merged` invalid: Schema default (`True`) does not match the config default (`false`) * [schema_params](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_params) - Default value for param `tracedir` invalid: Not in pipeline parameters. Check `nextflow.config`. * [schema_params](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_params) - Default value for param `validate_params` invalid: Schema default (`True`) does not match the config default (`false`) * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` does not contain a matching 'report_comment'. The expected comment is: ```This report has been generated by the nf-core/bacpaq analysis pipeline. For information about how to interpret these results, please see the documentation.``` The current comment is: ```bacpaq is a bioinformatics best-practice pipeline for bacterial genomic analysis for short-reads (Illumina) and long-reads (Oxford Nanopore) sequencing data. Currently bacpaq supports WGS-based analyses, however, we plan to integrate Microbiome (Amplicon and Shotgun Metagenomics) analyses in future.``` ### :heavy_exclamation_mark: Test warnings: * [schema_lint](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_lint) - Schema `$id` should be `https://raw.githubusercontent.com/cidgoh/bacpaq/master/nextflow_schema.json` Found `https://raw.githubusercontent.com/nf-core/bacpaq/master/nextflow_schema.json` * [schema_params](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_params) - Schema param `tracedir` not found from nextflow config * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - Ungrouped param in schema: `fasta` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `adapter_fasta` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_subsampling` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_confindr` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `save_merged` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `trim_tool` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `save_trimmed_fail` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `depth_cut_off` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `confindr_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_QC` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_raw_qc` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `subsampling_genomesize` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `classifier` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_combinekreports` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_kreport2krona` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_bracken` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_kraken2` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_combinebrackenoutputs` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_dehosting` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `kraken2_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `classified_reads` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `unclassified_reads` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `centrifuge_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `save_unaligned` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `save_aligned` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `dehosting_aligner` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `sam_format` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `bam_format` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `bwa_sort_bam` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `cigar_paf_format` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `cigar_bam` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `interleaved` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `host_genome` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `host_genome_id` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_taxonomy_qc` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `min_contig_len` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `min_contig_coverage` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `min_input_read_len` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `min_input_quality` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `racon_rounds` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `medaka_rounds` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `medaka_model` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `sr_assembler` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_assembly` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `assembly_genomesize` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `checkm_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `combine_quast` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `busco_lineage` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `busco_lineages_path` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `busco_config` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_checkm` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_quast` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_busco` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `reference_genome_fasta` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `reference_genome_gff` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_assembly_qc` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_rmlst` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_gene_annotation` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_prokka` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_bakta` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `bakta_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `prodigal_training_file` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `annotation_protein_file` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_pangenome_analysis` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `pangenome_input` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_roary` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_pirate` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_panaroo` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_peppan` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `clean_mode` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `reference_gff` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_plasmid_analysis` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_plasmidfinder` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_mobsuite` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_phage_annotation` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `virsorter_db` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `virsorter_virus_grp` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `virsorter_min_len` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `virsorter_min_score` * [schema_description](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_description) - No description provided in schema for parameter: `skip_cctyper` * [nfcore_yml](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nfcore_yml) - nf-core version not set in `.nf-core.yml` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `README.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `assets/nf-core-bacpaq_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `conf/test_full.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-bacpaq_logo_light.png` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/images/nf-core-bacpaq_logo_dark.png` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `main.nf` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `.github/workflows/awsfulltest.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File found: `modules.json` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `docs/images/nf-core-bacpaq_logo.png` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `lib/WorkflowBacpaq.groovy` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `pipeline_template.yml` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_exist) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.name` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.homePage` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config ``manifest.version`` ends in ``dev``: ``1.0dev`` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/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/2.14.1/pipeline_lint_tests/nextflow_config) - Lines for loading custom profiles found * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - nextflow.config contains configuration profile `test` * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.fasta= test.fa * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.nanopore_summary_file_id= test * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.trim_tool= fastp * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.confindr_db= /mnt/cidgoh-object-storage/database/confindr/confindr_db * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.subsampling_genomesize= 5000000 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.classifier= kraken2 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.kraken2_db= /mnt/cidgoh-object-storage/database/minikraken2/minikraken2_v2_8GB_201904_UPDATE * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.classified_reads= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.unclassified_reads= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.centrifuge_db= /mnt/cidgoh-object-storage/database/centrifuge * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.save_unaligned= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.save_aligned= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.dehosting_aligner= minimap2 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.sam_format= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.bam_format= true * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.bwa_sort_bam= sort * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.host_genome= /mnt/cidgoh-object-storage/database/reference_genomes/human/GRCh38.p14/GCF_000001405.40/GCF_000001405.40_GRCh38.p14_genomic.fna * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.host_genome_id= GRCh38 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_contig_len= 500 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_contig_coverage= 2 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_input_read_len= 1000 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.min_input_quality= 0 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.racon_rounds= 1 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.medaka_rounds= 1 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.medaka_model= r941_min_fast_g507 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.sr_assembler= spades * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.assembly_genomesize= \'\ * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.busco_lineage= bacteria * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.busco_lineages_path= /mnt/cidgoh-object-storage/database/busco * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.bakta_db= /mnt/cidgoh-object-storage/database/bakta/db/ * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.pangenome_input= bakta * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.clean_mode= moderate * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.virsorter_virus_grp= dsDNAphage,ssDNA * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.virsorter_min_len= 5000 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.virsorter_min_score= 0.4 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.abricate_db= card * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.resfinder_species= ecoli * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.custom_config_version= master * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/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/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_cpus= 16 * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_memory= 128.GB * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_time= 240.h * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.publish_dir_mode= copy * [nextflow_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nextflow_config) - Config default value correct: params.max_multiqc_email_size= 25.MB * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `LICENSE` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.gitignore` matches the template * [files_unchanged](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/files_unchanged) - `.prettierignore` matches the template * [actions_ci](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_ci) - '.github/workflows/ci.yml' is triggered on expected events * [actions_awstest](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_awstest) - '.github/workflows/awstest.yml' is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` is triggered correctly * [actions_awsfulltest](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_awsfulltest) - `.github/workflows/awsfulltest.yml` does not use `-profile test` * [readme](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/readme) - README Zenodo placeholder was replaced with DOI. * [pipeline_todos](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/pipeline_todos) - No TODO strings found * [pipeline_name_conventions](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/pipeline_name_conventions) - Name adheres to nf-core convention * [schema_lint](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_lint) - Schema lint passed * [schema_lint](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/schema_lint) - Input mimetype lint passed: 'text/csv' * [system_exit](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/system_exit) - No `System.exit` calls found * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awsfulltest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting_comment.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: awstest.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: release-announcements.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: download_pipeline.yml * [actions_schema_validation](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/actions_schema_validation) - Workflow validation passed: ci.yml * [merge_markers](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/merge_markers) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_json) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` found and not ignored. * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_section_order` * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `export_plots` * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains `report_comment` * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/multiqc_config) - `assets/multiqc_config.yml` contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_structure) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' * [base_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/base_config) - `conf/base.config` found and not ignored. * [base_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/base_config) - `CUSTOM_DUMPSOFTWAREVERSIONS` found in `conf/base.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `conf/modules.config` found and not ignored. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMPLESHEET_CHECK` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `CAT_NANOPORE_FASTQ` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PORECHOP_ABI` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `NANOCOMP` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PYCOQC` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RASUSA` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMTOOLS_VIEW` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMTOOLS_FASTQ` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMTOOLS_FLAGSTAT` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMTOOLS_SORT` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SAMTOOLS_INDEX` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `KRAKEN2_KRAKEN2` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `BRACKEN_BRACKEN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `KRAKENTOOLS_KREPORT2KRONA` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `CONFINDR` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `AGGREGATE_CONFINDR_RESULTS` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `MINIMAP2_ALIGN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RAW_FASTQC` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `TRIM_FASTQC` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `FASTP` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `KRONA_KTIMPORTTAXONOMY` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `KRONA_KTIMPORTTEXT` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `KRONA_KTUPDATETAXONOMY` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `MULTIQC` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `TRIMMOMATIC` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `DRAGONFLYE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `SHOVILL` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RENAME_CTG` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `QUAST` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `QUAST` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `BUSCO` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RMLST` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RMLSTPARSE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PROKKA` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `CHECKM_LINEAGEWF` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `BAKTA_BAKTADBDOWNLOAD` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `BAKTA_BAKTA` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `VIRSORTER2_RUN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `VIRSORTER2_SETUP` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PANAROO_RUN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `ROARY` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PIRATE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PEPPAN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `MOBSUITE_RECON` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `PLASMIDFINDER` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RESFINDER` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `ABRICATE_RUN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `ABRICATE_SUMMARY` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `AMRFINDERPLUS_UPDATE` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `AMRFINDERPLUS_RUN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `RGI_MAIN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `ABRITAMR_RUN` found in `conf/modules.config` and Nextflow scripts. * [modules_config](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/modules_config) - `CCTYPER` found in `conf/modules.config` and Nextflow scripts. * [nfcore_yml](https://nf-co.re/tools/docs/2.14.1/pipeline_lint_tests/nfcore_yml) - Repository type in `.nf-core.yml` is valid: `pipeline` ### Run details * nf-core/tools version 2.14.1 * Run at `2024-06-25 05:55:14`