fix dead link #1395

allaway · 2024-02-07T14:34:41Z

Just fixing a dead link I came across :)

PR checklist

This comment contains a description of changes (with reason).
README.md is updated (including new tool citations and authors/contributors).

FriederikeHanssen

thanks for the fix :)

github-actions · 2024-02-07T14:39:58Z

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

Posted for pipeline commit 6b32335

+| ✅ 188 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   2 tests had warnings |!

Details

❗ Test warnings:

files_exist - File not found: .github/workflows/awstest.yml
pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

files_exist - File is ignored: .github/workflows/awsfulltest.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: lib/NfcoreTemplate.groovy
actions_ci - actions_ci
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
template_strings - template_strings

✅ 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-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: lib/NfcoreTemplate.groovy
files_exist - File found: lib/Utils.groovy
files_exist - File found: lib/WorkflowMain.groovy
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: lib/WorkflowSarek.groovy
files_exist - File found: modules.json
files_exist - File found: pyproject.toml
files_exist - File not found check: Singularity
files_exist - File not found check: parameters.settings.json
files_exist - File not found check: pipeline_template.yml
files_exist - File not found check: .nf-core.yaml
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: .github/workflows/push_dockerhub.yml
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: docs/images/nf-core-sarek_logo.png
files_exist - File not found check: .markdownlint.yml
files_exist - File not found check: .yamllint.yml
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/Workflow.groovy
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: 3.5dev
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.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.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= 110.0-0
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.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
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
files_unchanged - .gitignore matches the template
files_unchanged - .prettierignore matches the template
files_unchanged - pyproject.toml matches the template
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
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: cloudtest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: ci.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: ncbench.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: download_pipeline.yml
actions_schema_validation - Workflow validation passed: fix-linting.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' 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'

Run details

nf-core/tools version 2.12.1
Run at 2024-02-07 14:39:41

fix dead link

0916676

allaway requested review from FriederikeHanssen and maxulysse as code owners February 7, 2024 14:34

add back dropped parens

6b32335

FriederikeHanssen approved these changes Feb 7, 2024

View reviewed changes

maxulysse merged commit a56f0be into nf-core:dev Feb 14, 2024

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fix dead link #1395

fix dead link #1395

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allaway commented Feb 7, 2024 •

edited

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github-actions bot commented Feb 7, 2024

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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fix dead link #1395

fix dead link #1395

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allaway commented Feb 7, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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github-actions bot commented Feb 7, 2024

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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allaway commented Feb 7, 2024 •

edited

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