Added additional reports to Tower output

Open mschaffer-incyte opened this issue 1 year ago • 2 comments

Added additional reports for targeted analysis to tower.yml so the outputs appear in the reports tab of Tower installations.

Apr 25 '24 17:04 mschaffer-incyte

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

Posted for pipeline commit fd82bb2

+| ✅ 222 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   5 tests had warnings |!

:heavy_exclamation_mark: Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.2.0
pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

:grey_question: Tests ignored:

files_exist - File is ignored: conf/test.config
files_exist - File is ignored: conf/test_full.config
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md

: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
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: assets/nf-core-crisprseq_logo_light.png
files_exist - File found: conf/modules.config
files_exist - File found: docs/images/nf-core-crisprseq_logo_light.png
files_exist - File found: docs/images/nf-core-crisprseq_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
files_exist - File not found check: .nf-core.yaml
files_exist - File not found check: .yamllint.yml
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-crisprseq_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/WorkflowCrisprseq.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 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.umi_bin_size= 1
nextflow_config - Config default value correct: params.medaka_model= r941_min_high_g303
nextflow_config - Config default value correct: params.aligner= minimap2
nextflow_config - Config default value correct: params.vsearch_minseqlength= 55
nextflow_config - Config default value correct: params.vsearch_maxseqlength= 57
nextflow_config - Config default value correct: params.vsearch_id= 0.99
nextflow_config - Config default value correct: params.min_reads= 30.0
nextflow_config - Config default value correct: params.min_targeted_genes= 3.0
nextflow_config - Config default value correct: params.bagel_reference_essentials= https://raw.githubusercontent.com/hart-lab/bagel/master/CEGv2.txt
nextflow_config - Config default value correct: params.bagel_reference_nonessentials= https://raw.githubusercontent.com/hart-lab/bagel/master/NEGv1.txt
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.validationSchemaIgnoreParams= genomes,igenomes_base
nextflow_config - Config default value correct: params.pipelines_testdata_base_path= https://raw.githubusercontent.com/nf-core/test-datasets/
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/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-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_logo_light.png matches the template
files_unchanged - docs/images/nf-core-crisprseq_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 (268 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: branch.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: awsfulltest_screening.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.
modules_config - conf/modules.config found and not ignored.
modules_config - ORIENT_REFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - CAT_FASTQ found in conf/modules.config and Nextflow scripts.
modules_config - PEAR found in conf/modules.config and Nextflow scripts.
modules_config - BAGEL2_BF found in conf/modules.config and Nextflow scripts.
modules_config - BAGEL2_PR found in conf/modules.config and Nextflow scripts.
modules_config - BAGEL2_FC found in conf/modules.config and Nextflow scripts.
modules_config - BAGEL2_GRAPH found in conf/modules.config and Nextflow scripts.
modules_config - FASTQC found in conf/modules.config and Nextflow scripts.
modules_config - FIND_ADAPTERS found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_COUNT found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_MLE found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_TEST found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_GRAPHRRA found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_FLUTEMLE found in conf/modules.config and Nextflow scripts.
modules_config - VENNDIAGRAM found in conf/modules.config and Nextflow scripts.
modules_config - MAGECK_MLE_DAY0 found in conf/modules.config and Nextflow scripts.
modules_config - CRISPRCLEANR_NORMALIZE found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_FIVE_PRIME found in conf/modules.config and Nextflow scripts.
modules_config - CUTADAPT_THREE_PRIME found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SEQ_MASK found in conf/modules.config and Nextflow scripts.
modules_config - EXTRACT_UMIS found in conf/modules.config and Nextflow scripts.
modules_config - VSEARCH_CLUSTER found in conf/modules.config and Nextflow scripts.
modules_config - VSEARCH_SORT found in conf/modules.config and Nextflow scripts.
modules_config - PREPROCESSING_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - MATRICESCREATION found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN_UMI_1 found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN_UMI_2 found in conf/modules.config and Nextflow scripts.
modules_config - RACON_1 found in conf/modules.config and Nextflow scripts.
modules_config - RACON_2 found in conf/modules.config and Nextflow scripts.
modules_config - MEDAKA found in conf/modules.config and Nextflow scripts.
modules_config - SEQTK_SEQ_FATOFQ found in conf/modules.config and Nextflow scripts.
modules_config - CLUSTERING_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN_ORIGINAL found in conf/modules.config and Nextflow scripts.
modules_config - ALIGNMENT_SUMMARY found in conf/modules.config and Nextflow scripts.
modules_config - SAMTOOLS_INDEX found in conf/modules.config and Nextflow scripts.
modules_config - TEMPLATE_REFERENCE found in conf/modules.config and Nextflow scripts.
modules_config - MINIMAP2_ALIGN_TEMPLATE found in conf/modules.config and Nextflow scripts.
modules_config - CIGAR_PARSER found in conf/modules.config and Nextflow scripts.
modules_config - CRISPRSEQ_PLOTTER 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