NotificationsYou must be signed in to change notification settings
Fork490
Star503

Add full test report#1701

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to ourterms of service andprivacy statement. We’ll occasionally send you account related emails.

Already on GitHub?Sign in to your account

Jump to bottom

Draft

edmundmiller wants to merge3 commits intodev

base:dev

Choose a base branch

fromtest-report

Draft

Add full test report#1701

edmundmiller wants to merge3 commits intodevfromtest-report

Conversation

Copy link

Contributor

edmundmiller commentedOct 28, 2024

Closes#1699

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 thecontribution docs
If necessary, also make a PR on the nf-core/sarekbranch on thenf-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 indocs/usage.md is updated.
Output Documentation indocs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

edmundmiller self-assigned this

Oct 28, 2024

edmundmiller changed the base branch frommaster todev

October 28, 2024 10:42

Copy link

github-actionsbot commentedOct 28, 2024•
edited
Loading

`nf-core pipelines lint` overall result: Passed ✅⚠️

Posted for pipeline commitab64cb2

+| ✅ 216 tests passed       |+#| ❔  11 tests were ignored |#!| ❗   4 tests had warnings |!

❗ Test warnings:

pipeline_todos - TODO string inmain.nf:Optionally add in-text citation tools to this list.
pipeline_todos - TODO string inmain.nf:Optionally add bibliographic entries to this list.
pipeline_todos - TODO string inmain.nf:Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
pipeline_todos - TODO string inbase.config:Check the defaults for all processes

❔ Tests ignored:

files_exist - File is ignored:.github/workflows/awsfulltest.yml
files_exist - File is ignored:.github/workflows/awstest.yml
files_exist - File is ignored:conf/modules.config
files_unchanged - File ignored due to lint config:assets/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config:docs/images/nf-core-sarek_logo_light.png
files_unchanged - File ignored due to lint config:docs/images/nf-core-sarek_logo_dark.png
files_unchanged - File ignored due to lint config:.gitignore or.prettierignore
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found:/home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings
modules_config - modules_config

✅ 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 orLICENSE.md orLICENCE orLICENCE.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-sarek_logo_light.png
files_exist - File found:conf/test.config
files_exist - File found:conf/test_full.config
files_exist - File found:docs/images/nf-core-sarek_logo_light.png
files_exist - File found:docs/images/nf-core-sarek_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:conf/igenomes_ignored.config
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-sarek_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/WorkflowSarek.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 - Found nf-schema plugin
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:validation.help.enabled
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 found:validation.help.beforeText
nextflow_config - Config variable found:validation.help.afterText
nextflow_config - Config variable found:validation.help.command
nextflow_config - Config variable found:validation.summary.beforeText
nextflow_config - Config variable found:validation.summary.afterText
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 variable (correctly) not found:params.max_cpus
nextflow_config - Config variable (correctly) not found:params.max_memory
nextflow_config - Config variable (correctly) not found:params.max_time
nextflow_config - Config variable (correctly) not found:params.validationFailUnrecognisedParams
nextflow_config - Config variable (correctly) not found:params.validationLenientMode
nextflow_config - Config variable (correctly) not found:params.validationSchemaIgnoreParams
nextflow_config - Config variable (correctly) not found:params.validationShowHiddenParams
nextflow_config - Configtimeline.enabled had correct value:true
nextflow_config - Configreport.enabled had correct value:true
nextflow_config - Configtrace.enabled had correct value:true
nextflow_config - Configdag.enabled had correct value:true
nextflow_config - Configmanifest.name began withnf-core/
nextflow_config - Config variablemanifest.homePage began withhttps://github.com/nf-core/
nextflow_config - Configdag.file ended with.html
nextflow_config - Config variablemanifest.nextflowVersion started with >= or !>=
nextflow_config - Configmanifest.version ends indev:3.5.0dev
nextflow_config - Configparams.custom_config_version is set tomaster
nextflow_config - Configparams.custom_config_base is set tohttps://raw.githubusercontent.com/nf-core/configs/master
nextflow_config - Lines for loading custom profiles found
nextflow_config - nextflow.config contains configuration profiletest
nextflow_config - Config default value correct: params.step= mapping
nextflow_config - Config default value correct: params.split_fastq= 50000000
nextflow_config - Config default value correct: params.nucleotides_per_second= 200000
nextflow_config - Config default value correct: params.clip_r1= 0
nextflow_config - Config default value correct: params.clip_r2= 0
nextflow_config - Config default value correct: params.three_prime_clip_r1= 0
nextflow_config - Config default value correct: params.three_prime_clip_r2= 0
nextflow_config - Config default value correct: params.trim_nextseq= 0
nextflow_config - Config default value correct: params.length_required= 15
nextflow_config - Config default value correct: params.group_by_umi_strategy= Adjacency
nextflow_config - Config default value correct: params.aligner= bwa-mem
nextflow_config - Config default value correct: params.ascat_min_base_qual= 20
nextflow_config - Config default value correct: params.ascat_min_counts= 10
nextflow_config - Config default value correct: params.ascat_min_map_qual= 35
nextflow_config - Config default value correct: params.cf_coeff= 0.05
nextflow_config - Config default value correct: params.cf_contamination= 0
nextflow_config - Config default value correct: params.cf_minqual= 0
nextflow_config - Config default value correct: params.cf_mincov= 0
nextflow_config - Config default value correct: params.cf_ploidy= 2
nextflow_config - Config default value correct: params.sentieon_haplotyper_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_emit_mode= variant
nextflow_config - Config default value correct: params.sentieon_dnascope_pcr_indel_model= CONSERVATIVE
nextflow_config - Config default value correct: params.dbnsfp_fields= rs_dbSNP,HGVSc_VEP,HGVSp_VEP,1000Gp3_EAS_AF,1000Gp3_AMR_AF,LRT_score,GERP++_RS,gnomAD_exomes_AF
nextflow_config - Config default value correct: params.vep_custom_args= --everything --filter_common --per_gene --total_length --offline --format vcf
nextflow_config - Config default value correct: params.vep_version= 111.0-0
nextflow_config - Config default value correct: params.vep_out_format= vcf
nextflow_config - Config default value correct: params.genome= GATK.GRCh38
nextflow_config - Config default value correct: params.igenomes_base= s3://ngi-igenomes/igenomes/
nextflow_config - Config default value correct: params.vep_cache= s3://annotation-cache/vep_cache/
nextflow_config - Config default value correct: params.snpeff_cache= s3://annotation-cache/snpeff_cache/
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.test_data_base=https://raw.githubusercontent.com/nf-core/test-datasets/sarek3
nextflow_config - Config default value correct: params.seq_platform= ILLUMINA
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/
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 -docs/README.md matches the template
readme - README Nextflow minimum version badge matched config. Badge:24.04.2, Config:24.04.2
readme - README Zenodo placeholder was replaced with DOI.
plugin_includes - No wrong validation plugin imports have been found
pipeline_name_conventions - Name adheres to nf-core convention
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 - NoSystem.exit calls found
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: fix-linting.yml
actions_schema_validation - Workflow validation passed: release-announcements.yml
actions_schema_validation - Workflow validation passed: template_version_comment.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: ncbench.yml
actions_schema_validation - Workflow validation passed: test-report.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: cloudtest.yml
actions_schema_validation - Workflow validation passed: pytest.yml
actions_schema_validation - Workflow validation passed: clean-up.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
merge_markers - No merge markers found in pipeline files
modules_json - Only installed modules found inmodules.json
multiqc_config -assets/multiqc_config.yml found and not ignored.
multiqc_config -assets/multiqc_config.yml containsreport_section_order
multiqc_config -assets/multiqc_config.yml containsexport_plots
multiqc_config -assets/multiqc_config.yml containsreport_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 -UNZIP found inconf/base.config and Nextflow scripts.
base_config -FASTQC found inconf/base.config and Nextflow scripts.
base_config -FASTP found inconf/base.config and Nextflow scripts.
base_config -BWAMEM1_MEM found inconf/base.config and Nextflow scripts.
base_config -CNVKIT_BATCH found inconf/base.config and Nextflow scripts.
base_config -GATK4_MARKDUPLICATES found inconf/base.config and Nextflow scripts.
base_config -GATK4_APPLYBQSR found inconf/base.config and Nextflow scripts.
base_config -MOSDEPTH found inconf/base.config and Nextflow scripts.
base_config -STRELKA found inconf/base.config and Nextflow scripts.
base_config -SAMTOOLS_CONVERT found inconf/base.config and Nextflow scripts.
base_config -GATK4_MERGEVCFS found inconf/base.config and Nextflow scripts.
base_config -MULTIQC found inconf/base.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:3.0.2