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add customized multiqc config file #62

Merged
merged 11 commits into from
Jun 25, 2024
Merged

add customized multiqc config file #62

merged 11 commits into from
Jun 25, 2024

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azmigueldario
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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.

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github-actions bot commented May 3, 2024

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 👍

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github-actions bot commented May 3, 2024 •
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 10f4c27

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

❌ Test failures:

  • files_exist - File must be removed: lib/Utils.groovy
  • files_exist - File not found check: lib/nfcore_external_java_deps.jar
  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • nextflow_config - Config manifest.name did not begin with nf-core/:
    cidgoh/bacpaq
  • nextflow_config - Config variable manifest.homePage did not begin with https://github.com/nf-core/:
    https://github.com/cidgoh/bacpaq
  • nextflow_config - Config default value incorrect: params.mode is set as illumina in nextflow_schema.json but is nanopore in nextflow.config.
  • 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 - Config default value incorrect: params.skip_subsampling is set as true in nextflow_schema.json but is false in nextflow.config.
  • 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 - 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 - Default value from the Nextflow schema params.tracedir = 25.MB`` not found in nextflow.config.
  • 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 - Config default value incorrect: params.schema_ignore_params is set as fasta in nextflow_schema.json but is genomes in nextflow.config.
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml does not match the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
  • files_unchanged - .github/workflows/branch.yml does not match the template
  • files_unchanged - .github/workflows/linting_comment.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/email_template.html does not match the template
  • files_unchanged - assets/email_template.txt does not match the template
  • files_unchanged - assets/sendmail_template.txt does not match the template
  • files_unchanged - docs/README.md does not match the template
  • actions_ci - Minimum pipeline NF version '22.01.0' is not tested in '.github/workflows/ci.yml'
  • readme - README Nextflow minimum version badge does not match config. Badge: 23.04.0, Config: 22.01.0
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/modules/local/RMLST/ubuntu_curl_test.sif L319578: b{{XmwçDç�Ë{«=4�¼Ö¶?fÍÛp�Õ}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-angular.mjs L2: "{{","}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-angular.mjs L2: "{{",I="}}
  • 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 - 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 - 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 - 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 - 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 - 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{ "+this.SubExpression(l)+" }}
  • 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{^}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{> "+e+" }}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L12: "{{> "+e+" }}
  • 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L26: `{{${(0,c.printLiteral)(b)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L27: ({{> ...}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L27: `{{#${M.path}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-glimmer.mjs L27: `{{#${C.path}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-html.mjs L34: "{{","}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-html.mjs L35: "{{ '{' }}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/parser-markdown.mjs L75: |{{.*?}}
  • 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs L107: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs L110: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/esm/standalone.mjs L110: "{{",d(Z),"}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js L32245: "{{", printPathAndParams(path, print2), "}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js L35748: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js L36588: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/index.js L36602: "{{", replaceTextEndOfLine(part), "}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-angular.js L2: "{{","}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-angular.js L2: "{{",I="}}
  • 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 - 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 - 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 - 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 - 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 - 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L12: "{{ "+this.SubExpression(o)+" }}
  • 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L12: "{{^}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L12: "{{> "+e+" }}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L12: "{{> "+e+" }}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L12: "{{! '"+o.value+"' }}
  • 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 - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L27: ({{> ...}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L27: `{{#${M.path}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-glimmer.js L27: `{{#${C.path}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-html.js L34: "{{","}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-html.js L35: "{{ '{' }}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/parser-markdown.js L75: |{{.*?}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js L75: "{{",Re(H,X),"}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js L107: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js L110: /{{(.+?)}}
  • template_strings - Found a Jinja template string in /home/runner/work/bacpaq/bacpaq/node_modules/prettier/standalone.js L110: "{{",y(Z),"}}
  • schema_params - Default value for param skip_subsampling invalid: Schema default (True) does not match the config default (false)
  • schema_params - Default value for param save_merged invalid: Schema default (True) does not match the config default (false)
  • schema_params - Default value for param tracedir invalid: Not in pipeline parameters. Check nextflow.config.
  • schema_params - Default value for param validate_params invalid: Schema default (True) does not match the config default (false)
  • multiqc_config - assets/multiqc_config.yml does not contain a matching 'report_comment'.
    The expected comment is:
    This report has been generated by the <a href="https://github.com/nf-core/bacpaq/tree/dev" target="_blank">nf-core/bacpaq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/bacpaq/dev/docs/output" target="_blank">documentation</a>.
    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.

❗ Test warnings:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-25 05:55:14

@anwarMZ anwarMZ requested a review from jimmyliu1326 June 25, 2024 05:53
jimmyliu1326
jimmyliu1326 approved these changes Jun 25, 2024
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Confirmed that the pipeline runs to completion without any errors. Great stuff!

I did notice some minor formatting issues with the MultiQC report, but I feel we can let that slide for now:

  • If there are two FastQC sections displaying the read stats before/after preprocessing, then why are there six samples in each FastQC diagram? I'm expecting 3 samples, as the nanopore data is not analyzed by FastQC.
  • The general statistics table has too many missing values making it hard to understand. Likely need to split it into multiple tables

@anwarMZ anwarMZ merged commit dd06226 into dev Jun 25, 2024
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@jimmyliu1326 jimmyliu1326 jimmyliu1326 approved these changes

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3 participants
@azmigueldario @jimmyliu1326 @anwarMZ