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Published 20 hours ago • verified publisher icon nf-core

Add the column db_type to database sheet

Open LilyAnderssonLee opened this issue 10 months ago • 1 comments

Fix the issue https://github.com/nf-core/taxprofiler/issues/226

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/taxprofiler 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>).
  • [ ] Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

LilyAnderssonLee avatar Apr 08 '24 13:04 LilyAnderssonLee

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

Posted for pipeline commit 2534c08

+| ✅ 261 tests passed       |+
!| ❗   2 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in ci.yml: You can customise CI pipeline run tests as required

:white_check_mark: Tests passed:

  • files_exist - File found: .gitattributes
  • files_exist - File found: .gitignore
  • files_exist - File found: .nf-core.yml
  • files_exist - File found: .editorconfig
  • files_exist - File found: .prettierignore
  • files_exist - File found: .prettierrc.yml
  • files_exist - File found: CHANGELOG.md
  • files_exist - File found: CITATIONS.md
  • files_exist - File found: CODE_OF_CONDUCT.md
  • files_exist - File found: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_exist - File found: nextflow_schema.json
  • files_exist - File found: nextflow.config
  • files_exist - File found: README.md
  • files_exist - File found: .github/.dockstore.yml
  • files_exist - File found: .github/CONTRIBUTING.md
  • files_exist - File found: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
  • files_exist - File found: .github/workflows/branch.yml
  • files_exist - File found: .github/workflows/ci.yml
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  • files_exist - File found: .github/workflows/linting.yml
  • files_exist - File found: assets/email_template.html
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  • files_exist - File found: assets/nf-core-taxprofiler_logo_light.png
  • files_exist - File found: conf/modules.config
  • files_exist - File found: conf/test.config
  • files_exist - File found: conf/test_full.config
  • files_exist - File found: docs/images/nf-core-taxprofiler_logo_light.png
  • files_exist - File found: docs/images/nf-core-taxprofiler_logo_dark.png
  • files_exist - File found: docs/output.md
  • files_exist - File found: docs/README.md
  • files_exist - File found: docs/README.md
  • files_exist - File found: docs/usage.md
  • files_exist - File found: main.nf
  • files_exist - File found: assets/multiqc_config.yml
  • files_exist - File found: conf/base.config
  • files_exist - File found: conf/igenomes.config
  • files_exist - File found: .github/workflows/awstest.yml
  • files_exist - File found: .github/workflows/awsfulltest.yml
  • files_exist - File found: modules.json
  • files_exist - File not found check: .github/ISSUE_TEMPLATE/bug_report.md
  • files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
  • files_exist - File not found check: .github/workflows/push_dockerhub.yml
  • files_exist - File not found check: .markdownlint.yml
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  • files_exist - File not found check: bin/markdown_to_html.r
  • files_exist - File not found check: conf/aws.config
  • files_exist - File not found check: docs/images/nf-core-taxprofiler_logo.png
  • files_exist - File not found check: lib/Checks.groovy
  • files_exist - File not found check: lib/Completion.groovy
  • files_exist - File not found check: lib/NfcoreTemplate.groovy
  • files_exist - File not found check: lib/Utils.groovy
  • files_exist - File not found check: lib/Workflow.groovy
  • files_exist - File not found check: lib/WorkflowMain.groovy
  • files_exist - File not found check: lib/WorkflowTaxprofiler.groovy
  • files_exist - File not found check: parameters.settings.json
  • files_exist - File not found check: pipeline_template.yml
  • files_exist - File not found check: Singularity
  • files_exist - File not found check: lib/nfcore_external_java_deps.jar
  • files_exist - File not found check: .travis.yml
  • nextflow_config - Config variable found: manifest.name
  • nextflow_config - Config variable found: manifest.nextflowVersion
  • nextflow_config - Config variable found: manifest.description
  • nextflow_config - Config variable found: manifest.version
  • nextflow_config - Config variable found: manifest.homePage
  • nextflow_config - Config variable found: timeline.enabled
  • nextflow_config - Config variable found: trace.enabled
  • nextflow_config - Config variable found: report.enabled
  • nextflow_config - Config variable found: dag.enabled
  • nextflow_config - Config variable found: process.cpus
  • nextflow_config - Config variable found: process.memory
  • nextflow_config - Config variable found: process.time
  • nextflow_config - Config variable found: params.outdir
  • nextflow_config - Config variable found: params.input
  • nextflow_config - Config variable found: params.validationShowHiddenParams
  • nextflow_config - Config variable found: params.validationSchemaIgnoreParams
  • nextflow_config - Config variable found: manifest.mainScript
  • nextflow_config - Config variable found: timeline.file
  • nextflow_config - Config variable found: trace.file
  • nextflow_config - Config variable found: report.file
  • nextflow_config - Config variable found: dag.file
  • nextflow_config - Config variable (correctly) not found: params.nf_required_version
  • nextflow_config - Config variable (correctly) not found: params.container
  • nextflow_config - Config variable (correctly) not found: params.singleEnd
  • nextflow_config - Config variable (correctly) not found: params.igenomesIgnore
  • nextflow_config - Config variable (correctly) not found: params.name
  • nextflow_config - Config variable (correctly) not found: params.enable_conda
  • nextflow_config - Config timeline.enabled had correct value: true
  • nextflow_config - Config report.enabled had correct value: true
  • nextflow_config - Config trace.enabled had correct value: true
  • nextflow_config - Config dag.enabled had correct value: true
  • nextflow_config - Config manifest.name began with nf-core/
  • nextflow_config - Config variable manifest.homePage began with https://github.com/nf-core/
  • nextflow_config - Config dag.file ended with .html
  • nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
  • nextflow_config - Config manifest.version ends in dev: 1.1.8dev
  • nextflow_config - Config params.custom_config_version is set to master
  • nextflow_config - Config params.custom_config_base is set to https://raw.githubusercontent.com/nf-core/configs/master
  • nextflow_config - Lines for loading custom profiles found
  • nextflow_config - nextflow.config contains configuration profile test
  • nextflow_config - Config default value correct: params.preprocessing_qc_tool= fastqc
  • nextflow_config - Config default value correct: params.shortread_qc_tool= fastp
  • nextflow_config - Config default value correct: params.shortread_qc_minlength= 15
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_tool= bbduk
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_entropy= 0.3
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_bbduk_windowsize= 50
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_fastp_threshold= 30
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_mode= entropy
  • nextflow_config - Config default value correct: params.shortread_complexityfilter_prinseqplusplus_dustscore= 0.5
  • nextflow_config - Config default value correct: params.longread_qc_qualityfilter_minlength= 1000
  • nextflow_config - Config default value correct: params.longread_qc_qualityfilter_keeppercent= 90
  • nextflow_config - Config default value correct: params.longread_qc_qualityfilter_targetbases= 500000000
  • nextflow_config - Config default value correct: params.shortread_redundancyestimation_mode= kmer
  • nextflow_config - Config default value correct: params.diamond_output_format= tsv
  • nextflow_config - Config default value correct: params.kaiju_taxon_rank= species
  • nextflow_config - Config default value correct: params.krakenuniq_ram_chunk_size= 16G
  • nextflow_config - Config default value correct: params.krakenuniq_batch_size= 20
  • nextflow_config - Config default value correct: params.malt_mode= BlastN
  • nextflow_config - Config default value correct: params.ganon_report_type= reads
  • nextflow_config - Config default value correct: params.ganon_report_toppercentile= 0
  • nextflow_config - Config default value correct: params.ganon_report_mincount= 0
  • nextflow_config - Config default value correct: params.ganon_report_maxcount= 0
  • nextflow_config - Config default value correct: params.standardisation_taxpasta_format= tsv
  • nextflow_config - Config default value correct: params.custom_config_version= master
  • nextflow_config - Config default value correct: params.custom_config_base= https://raw.githubusercontent.com/nf-core/configs/master
  • nextflow_config - Config default value correct: params.max_cpus= 16
  • nextflow_config - Config default value correct: params.max_memory= 128.GB
  • nextflow_config - Config default value correct: params.max_time= 240.h
  • nextflow_config - Config default value correct: params.publish_dir_mode= copy
  • nextflow_config - Config default value correct: params.max_multiqc_email_size= 25.MB
  • nextflow_config - Config default value correct: params.validate_params= true
  • nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
  • nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
  • files_unchanged - .gitattributes matches the template
  • files_unchanged - .prettierrc.yml matches the template
  • files_unchanged - CODE_OF_CONDUCT.md matches the template
  • files_unchanged - LICENSE matches the template
  • files_unchanged - .github/.dockstore.yml matches the template
  • files_unchanged - .github/CONTRIBUTING.md matches the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml matches the template
  • files_unchanged - .github/ISSUE_TEMPLATE/config.yml matches the template
  • files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml matches the template
  • files_unchanged - .github/PULL_REQUEST_TEMPLATE.md matches the template
  • files_unchanged - .github/workflows/branch.yml matches the template
  • files_unchanged - .github/workflows/linting_comment.yml matches the template
  • files_unchanged - .github/workflows/linting.yml matches the template
  • files_unchanged - assets/email_template.html matches the template
  • files_unchanged - assets/email_template.txt matches the template
  • files_unchanged - assets/sendmail_template.txt matches the template
  • files_unchanged - assets/nf-core-taxprofiler_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-taxprofiler_logo_light.png matches the template
  • files_unchanged - docs/images/nf-core-taxprofiler_logo_dark.png matches the template
  • files_unchanged - docs/README.md matches the template
  • files_unchanged - .gitignore matches the template
  • files_unchanged - .prettierignore matches the template
  • actions_ci - '.github/workflows/ci.yml' is triggered on expected events
  • actions_ci - '.github/workflows/ci.yml' checks minimum NF version
  • actions_awstest - '.github/workflows/awstest.yml' is triggered correctly
  • actions_awsfulltest - .github/workflows/awsfulltest.yml is triggered correctly
  • actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
  • readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
  • readme - README Zenodo placeholder was replaced with DOI.
  • pipeline_name_conventions - Name adheres to nf-core convention
  • template_strings - Did not find any Jinja template strings (296 files)
  • schema_lint - Schema lint passed
  • schema_lint - Schema title + description lint passed
  • schema_lint - Input mimetype lint passed: 'text/csv'
  • schema_params - Schema matched params returned from nextflow config
  • system_exit - No System.exit calls found
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: fix-linting.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
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  • actions_schema_validation - Workflow validation passed: download_pipeline.yml
  • actions_schema_validation - Workflow validation passed: ci.yml
  • merge_markers - No merge markers found in pipeline files
  • modules_json - Only installed modules found in modules.json
  • multiqc_config - assets/multiqc_config.yml found and not ignored.
  • multiqc_config - assets/multiqc_config.yml contains report_section_order
  • multiqc_config - assets/multiqc_config.yml contains export_plots
  • multiqc_config - assets/multiqc_config.yml contains report_comment
  • multiqc_config - assets/multiqc_config.yml follows the ordering scheme of the minimally required plugins.
  • multiqc_config - assets/multiqc_config.yml contains a matching 'report_comment'.
  • multiqc_config - assets/multiqc_config.yml contains 'export_plots: true'.
  • modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'
  • base_config - conf/base.config found and not ignored.
  • base_config - BRACKEN_BRACKEN found in conf/base.config and Nextflow scripts.
  • base_config - CENTRIFUGE_KREPORT found in conf/base.config and Nextflow scripts.
  • base_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/base.config and Nextflow scripts.
  • base_config - MEGAN_RMA2INFO_TSV found in conf/base.config and Nextflow scripts.
  • base_config - MEGAN_RMA2INFO_KRONA found in conf/base.config and Nextflow scripts.
  • base_config - FALCO found in conf/base.config and Nextflow scripts.
  • modules_config - conf/modules.config found and not ignored.
  • modules_config - UNTAR found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTQC_PROCESSED found in conf/modules.config and Nextflow scripts.
  • modules_config - FALCO found in conf/modules.config and Nextflow scripts.
  • modules_config - FALCO_PROCESSED found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTP_SINGLE found in conf/modules.config and Nextflow scripts.
  • modules_config - FASTP_PAIRED found in conf/modules.config and Nextflow scripts.
  • modules_config - ADAPTERREMOVAL_SINGLE found in conf/modules.config and Nextflow scripts.
  • modules_config - ADAPTERREMOVAL_PAIRED found in conf/modules.config and Nextflow scripts.
  • modules_config - NONPAREIL_NONPAREIL found in conf/modules.config and Nextflow scripts.
  • modules_config - NONPAREIL_CURVE found in conf/modules.config and Nextflow scripts.
  • modules_config - NONPAREIL_SET found in conf/modules.config and Nextflow scripts.
  • modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
  • modules_config - PORECHOP_PORECHOP found in conf/modules.config and Nextflow scripts.
  • modules_config - FILTLONG found in conf/modules.config and Nextflow scripts.
  • modules_config - BBMAP_BBDUK found in conf/modules.config and Nextflow scripts.
  • modules_config - PRINSEQPLUSPLUS found in conf/modules.config and Nextflow scripts.
  • modules_config - BOWTIE2_BUILD found in conf/modules.config and Nextflow scripts.
  • modules_config - BOWTIE2_ALIGN found in conf/modules.config and Nextflow scripts.
  • modules_config - MINIMAP2_INDEX found in conf/modules.config and Nextflow scripts.
  • modules_config - MINIMAP2_ALIGN found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_VIEW found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_FASTQ found in conf/modules.config and Nextflow scripts.
  • modules_config - SAMTOOLS_STATS found in conf/modules.config and Nextflow scripts.
  • modules_config - MERGE_RUNS found in conf/modules.config and Nextflow scripts.
  • modules_config - MALT_RUN found in conf/modules.config and Nextflow scripts.
  • modules_config - MEGAN_RMA2INFO_TSV found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKEN2_KRAKEN2 found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKEN2_STANDARD_REPORT found in conf/modules.config and Nextflow scripts.
  • modules_config - BRACKEN_BRACKEN found in conf/modules.config and Nextflow scripts.
  • modules_config - BRACKEN_COMBINEBRACKENOUTPUTS found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKENTOOLS_COMBINEKREPORTS_KRAKEN found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKENUNIQ_PRELOADEDKRAKENUNIQ found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKENTOOLS_KREPORT2KRONA found in conf/modules.config and Nextflow scripts.
  • modules_config - KRONA_CLEANUP found in conf/modules.config and Nextflow scripts.
  • modules_config - KRONA_KTIMPORTTEXT found in conf/modules.config and Nextflow scripts.
  • modules_config - MEGAN_RMA2INFO_KRONA found in conf/modules.config and Nextflow scripts.
  • modules_config - KRONA_KTIMPORTTAXONOMY found in conf/modules.config and Nextflow scripts.
  • modules_config - METAPHLAN_METAPHLAN found in conf/modules.config and Nextflow scripts.
  • modules_config - METAPHLAN_MERGEMETAPHLANTABLES found in conf/modules.config and Nextflow scripts.
  • modules_config - CENTRIFUGE_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
  • modules_config - CENTRIFUGE_KREPORT found in conf/modules.config and Nextflow scripts.
  • modules_config - KRAKENTOOLS_COMBINEKREPORTS_CENTRIFUGE found in conf/modules.config and Nextflow scripts.
  • modules_config - KAIJU_KAIJU found in conf/modules.config and Nextflow scripts.
  • modules_config - KAIJU_KAIJU2TABLE_SINGLE found in conf/modules.config and Nextflow scripts.
  • modules_config - KAIJU_KAIJU2TABLE_COMBINED found in conf/modules.config and Nextflow scripts.
  • modules_config - KAIJU_KAIJU2KRONA found in conf/modules.config and Nextflow scripts.
  • modules_config - DIAMOND_BLASTX found in conf/modules.config and Nextflow scripts.
  • modules_config - MOTUS_PROFILE found in conf/modules.config and Nextflow scripts.
  • modules_config - MOTUS_MERGE found in conf/modules.config and Nextflow scripts.
  • modules_config - KMCP_SEARCH found in conf/modules.config and Nextflow scripts.
  • modules_config - KMCP_PROFILE found in conf/modules.config and Nextflow scripts.
  • modules_config - GANON_CLASSIFY found in conf/modules.config and Nextflow scripts.
  • modules_config - GANON_REPORT found in conf/modules.config and Nextflow scripts.
  • modules_config - GANON_TABLE found in conf/modules.config and Nextflow scripts.
  • modules_config - TAXPASTA_MERGE found in conf/modules.config and Nextflow scripts.
  • modules_config - TAXPASTA_STANDARDISE found in conf/modules.config and Nextflow scripts.
  • modules_config - MULTIQC found in conf/modules.config and Nextflow scripts.
  • nfcore_yml - Repository type in .nf-core.yml is valid: pipeline
  • nfcore_yml - nf-core version in .nf-core.yml is set to the latest version: 2.14.1

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-25 06:45:50

github-actions[bot] avatar Apr 11 '24 07:04 github-actions[bot]

OK I made some changes to make the channel manipulation more 'nextflowy', namely using transpose to 'duplciate' a channel but each of one of the two having a different short/long types separately in each

I then modify both database and read channels to have type as a 'meta-meta', to allow them to combine, and then move the type back into the meta after combining

@LilyAnderssonLee please test when you have time to make sure I didn't get something compeltely wrong

jfy133 avatar Jun 20 '24 10:06 jfy133

@jfy133 I have run the tests for the test, test_full, and test_krakenuniq, and all of them passed. Great job! I think we can merge this PR once all tests pass.

LilyAnderssonLee avatar Jun 25 '24 06:06 LilyAnderssonLee

I forgot to check: did you check with an oldstyle samplesheet without the db_type column ? We wanted to make it optional and if so default to short;long right?

jfy133 avatar Jun 25 '24 06:06 jfy133