Skip to content
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.

Sign up for GitHub

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

Already on GitHub? Sign in to your account

Jump to bottom

fix: cadd_cache is a boolean #375

Merged
merged 1 commit into from
May 17, 2021
Merged

fix: cadd_cache is a boolean #375

merged 1 commit into from
May 17, 2021

Conversation

maxulysse
Copy link
Member

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 - add to the software_versions process and a regex to scrape_software_versions.py
    • 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/sarek 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).
  • 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).

@github-actions
Copy link

github-actions bot commented May 17, 2021 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit cdcd9cc

+| ✅ 262 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  29 tests had warnings |!

❗ Test warnings:

  • params_used - Config variable not found in main.nf: params.cpus
  • params_used - Config variable not found in main.nf: params.single_cpu_mem
  • actions_awsfulltest - .github/workflows/awsfulltest.yml should test full datasets, not -profile test
  • conda_env_yaml - Conda dep outdated: conda-forge::llvm-openmp=8.0.1=hc9558a2_0, 11.1.0 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1=py_0, 3.3.4 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0=py_0, 8.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.5.2=py_0, 2.9.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.9=ha228f0b_4, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::bwa-mem2=2.0=he513fc3_1, 2.2.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::cancerit-allelecount=4.0.2=ha228f0b_1, 4.2.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::cnvkit=0.9.6=py27_1, 0.9.8 available
  • conda_env_yaml - Conda dep outdated: bioconda::ensembl-vep=99.2=pl526hecc5488_0, 104.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::fgbio=1.1.0=0, 1.3.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2=py27h49fb759_2, 1.3.5 available
  • conda_env_yaml - Conda dep outdated: bioconda::gatk4-spark=4.1.7.0=0, 4.2.0.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::htslib=1.9=ha228f0b_7, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8=py_2, 1.10.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::samblaster=0.1.24=hc9558a2_3, 0.1.26 available
  • conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9=h10a08f8_12, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::snpeff=4.3.1t=0, 5.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::tiddit=2.7.1=py27hb3f55d8_1, 2.12.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::trim-galore=0.6.5=0, 0.6.6 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pigz=2.3.4=hed695b0_1, 2.6 available
  • conda_env_yaml - Conda dep outdated: conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1, 3.3.3 available
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in awstest.yml: You can customise CI pipeline run tests as required
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • schema_description - No description provided in schema for parameter: cpus

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo.png

✅ Tests passed:

  • files_exist - File found: .gitattributes
  • files_exist - File found: CHANGELOG.md
  • files_exist - File found: CODE_OF_CONDUCT.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.md
  • files_exist - File found: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.md
  • files_exist - File found: .github/markdownlint.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.png
  • files_exist - File found: bin/markdown_to_html.py
  • files_exist - File found: docs/images/nf-core-sarek_logo.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/nfcore_external_java_deps.jar
  • files_exist - File found: lib/NfcoreSchema.groovy
  • files_exist - File found: main.nf
  • files_exist - File found: environment.yml
  • files_exist - File found: Dockerfile
  • files_exist - File found: conf/base.config
  • files_exist - File found: .github/workflows/awstest.yml
  • files_exist - File found: .github/workflows/awsfulltest.yml
  • files_exist - File not found check: Singularity
  • files_exist - File not found check: parameters.settings.json
  • 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: .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.show_hidden_params
  • nextflow_config - Config variable found: params.schema_ignore_params
  • 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: process.container
  • nextflow_config - Config variable (correctly) not found: params.version
  • 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 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 .svg
  • nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
  • nextflow_config - Config process.container looks correct: nfcore/sarek:dev
  • nextflow_config - Config manifest.version ends in dev: '3.0dev'
  • 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
  • params_used - Config variable found in main.nf: params.input
  • params_used - Config variable found in main.nf: params.step
  • params_used - Config variable found in main.nf: params.genome
  • params_used - Config variable found in main.nf: params.genomes_base
  • params_used - Config variable found in main.nf: params.save_reference
  • params_used - Config variable found in main.nf: params.help
  • params_used - Config variable found in main.nf: params.no_intervals
  • params_used - Config variable found in main.nf: params.nucleotides_per_second
  • params_used - Config variable found in main.nf: params.sentieon
  • params_used - Config variable found in main.nf: params.skip_qc
  • params_used - Config variable found in main.nf: params.target_bed
  • params_used - Config variable found in main.nf: params.tools
  • params_used - Config variable found in main.nf: params.trim_fastq
  • params_used - Config variable found in main.nf: params.clip_r1
  • params_used - Config variable found in main.nf: params.clip_r2
  • params_used - Config variable found in main.nf: params.three_prime_clip_r1
  • params_used - Config variable found in main.nf: params.three_prime_clip_r2
  • params_used - Config variable found in main.nf: params.trim_nextseq
  • params_used - Config variable found in main.nf: params.save_trimmed
  • params_used - Config variable found in main.nf: params.split_fastq
  • params_used - Config variable found in main.nf: params.aligner
  • params_used - Config variable found in main.nf: params.markdup_java_options
  • params_used - Config variable found in main.nf: params.use_gatk_spark
  • params_used - Config variable found in main.nf: params.save_bam_mapped
  • params_used - Config variable found in main.nf: params.skip_markduplicates
  • params_used - Config variable found in main.nf: params.ascat_ploidy
  • params_used - Config variable found in main.nf: params.ascat_purity
  • params_used - Config variable found in main.nf: params.cf_coeff
  • params_used - Config variable found in main.nf: params.cf_contamination
  • params_used - Config variable found in main.nf: params.cf_contamination_adjustment
  • params_used - Config variable found in main.nf: params.cf_ploidy
  • params_used - Config variable found in main.nf: params.cf_window
  • params_used - Config variable found in main.nf: params.generate_gvcf
  • params_used - Config variable found in main.nf: params.no_strelka_bp
  • params_used - Config variable found in main.nf: params.pon
  • params_used - Config variable found in main.nf: params.pon_index
  • params_used - Config variable found in main.nf: params.ignore_soft_clipped_bases
  • params_used - Config variable found in main.nf: params.umi
  • params_used - Config variable found in main.nf: params.read_structure1
  • params_used - Config variable found in main.nf: params.read_structure2
  • params_used - Config variable found in main.nf: params.annotate_tools
  • params_used - Config variable found in main.nf: params.annotation_cache
  • params_used - Config variable found in main.nf: params.cadd_cache
  • params_used - Config variable found in main.nf: params.cadd_indels
  • params_used - Config variable found in main.nf: params.cadd_indels_tbi
  • params_used - Config variable found in main.nf: params.cadd_wg_snvs
  • params_used - Config variable found in main.nf: params.cadd_wg_snvs_tbi
  • params_used - Config variable found in main.nf: params.genesplicer
  • params_used - Config variable found in main.nf: params.snpeff_cache
  • params_used - Config variable found in main.nf: params.vep_cache
  • params_used - Config variable found in main.nf: params.config_profile_contact
  • params_used - Config variable found in main.nf: params.config_profile_description
  • params_used - Config variable found in main.nf: params.config_profile_url
  • params_used - Config variable found in main.nf: params.outdir
  • params_used - Config variable found in main.nf: params.publish_dir_mode
  • params_used - Config variable found in main.nf: params.sequencing_center
  • params_used - Config variable found in main.nf: params.multiqc_config
  • params_used - Config variable found in main.nf: params.monochrome_logs
  • params_used - Config variable found in main.nf: params.email
  • params_used - Config variable found in main.nf: params.email_on_fail
  • params_used - Config variable found in main.nf: params.plaintext_email
  • params_used - Config variable found in main.nf: params.max_multiqc_email_size
  • params_used - Config variable found in main.nf: params.hostnames
  • params_used - Config variable found in main.nf: params.validate_params
  • params_used - Config variable found in main.nf: params.tracedir
  • params_used - Config variable found in main.nf: params.max_cpus
  • params_used - Config variable found in main.nf: params.max_memory
  • params_used - Config variable found in main.nf: params.max_time
  • params_used - Config variable found in main.nf: params.fasta
  • params_used - Config variable found in main.nf: params.ac_loci
  • params_used - Config variable found in main.nf: params.ac_loci_gc
  • params_used - Config variable found in main.nf: params.bwa
  • params_used - Config variable found in main.nf: params.chr_dir
  • params_used - Config variable found in main.nf: params.chr_length
  • params_used - Config variable found in main.nf: params.dbsnp
  • params_used - Config variable found in main.nf: params.dbsnp_index
  • params_used - Config variable found in main.nf: params.dict
  • params_used - Config variable found in main.nf: params.fasta_fai
  • params_used - Config variable found in main.nf: params.germline_resource
  • params_used - Config variable found in main.nf: params.germline_resource_index
  • params_used - Config variable found in main.nf: params.intervals
  • params_used - Config variable found in main.nf: params.known_indels
  • params_used - Config variable found in main.nf: params.known_indels_index
  • params_used - Config variable found in main.nf: params.mappability
  • params_used - Config variable found in main.nf: params.snpeff_db
  • params_used - Config variable found in main.nf: params.species
  • params_used - Config variable found in main.nf: params.vep_cache_version
  • files_unchanged - .gitattributes 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/config.yml matches the template
  • files_unchanged - .github/markdownlint.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 - bin/markdown_to_html.py matches the template
  • files_unchanged - docs/README.md matches the template
  • files_unchanged - lib/nfcore_external_java_deps.jar matches the template
  • files_unchanged - lib/NfcoreSchema.groovy matches the template
  • files_unchanged - .gitignore matches the template
  • files_unchanged - .github/workflows/push_dockerhub_dev.yml matches the template
  • files_unchanged - .github/workflows/push_dockerhub_release.yml matches the template
  • files_unchanged - assets/multiqc_config.yaml matches the template
  • actions_ci - '.github/workflows/ci.yml' is triggered on expected events
  • actions_ci - CI is building the correct docker image: docker build --no-cache . -t nfcore/sarek:dev
  • actions_ci - CI is pulling the correct docker image: docker pull nfcore/sarek:dev
  • actions_ci - CI is tagging docker image correctly: docker tag nfcore/sarek:dev nfcore/sarek:dev
  • 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
  • readme - README Nextflow minimum version badge matched config. Badge: 20.04.0, Config: 20.04.0
  • readme - README had a bioconda badge
  • conda_env_yaml - Conda environment name was correct (nf-core-sarek-3.0dev)
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::llvm-openmp=8.0.1=hc9558a2_0
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::openmp=8.0.1=0
  • conda_env_yaml - Conda package is the latest available: conda-forge::openmp=8.0.1=0
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.1.1=py_0
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=6.0=py_0
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.5.2=py_0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::ascat=2.5.2=r40_2
  • conda_env_yaml - Conda package is the latest available: bioconda::ascat=2.5.2=r40_2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bcftools=1.9=ha228f0b_4
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bwa-mem2=2.0=he513fc3_1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17=hed695b0_7
  • conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17=hed695b0_7
  • conda_env_yaml - Conda dep had pinned version number: bioconda::cancerit-allelecount=4.0.2=ha228f0b_1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::cnvkit=0.9.6=py27_1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::control-freec=11.6=he1b5a44_0
  • conda_env_yaml - Conda package is the latest available: bioconda::control-freec=11.6=he1b5a44_0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::ensembl-vep=99.2=pl526hecc5488_0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9=0
  • conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::fgbio=1.1.0=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.2=py27h49fb759_2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4-spark=4.1.7.0=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::genesplicer=1.0=1
  • conda_env_yaml - Conda package is the latest available: bioconda::genesplicer=1.0=1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::htslib=1.9=ha228f0b_7
  • conda_env_yaml - Conda dep had pinned version number: bioconda::manta=1.6.0=py27_0
  • conda_env_yaml - Conda package is the latest available: bioconda::manta=1.6.0=py27_0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::msisensor=0.5=h25a10a7_1
  • conda_env_yaml - Conda package is the latest available: bioconda::msisensor=0.5=h25a10a7_1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.8=py_2
  • conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d=1
  • conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d=1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::samblaster=0.1.24=hc9558a2_3
  • conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.9=h10a08f8_12
  • conda_env_yaml - Conda dep had pinned version number: bioconda::snpeff=4.3.1t=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::strelka=2.9.10=0
  • conda_env_yaml - Conda package is the latest available: bioconda::strelka=2.9.10=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::tiddit=2.7.1=py27hb3f55d8_1
  • conda_env_yaml - Conda dep had pinned version number: bioconda::trim-galore=0.6.5=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::vcfanno=0.3.2=0
  • conda_env_yaml - Conda package is the latest available: bioconda::vcfanno=0.3.2=0
  • conda_env_yaml - Conda dep had pinned version number: bioconda::vcftools=0.1.16=he513fc3_4
  • conda_env_yaml - Conda package is the latest available: bioconda::vcftools=0.1.16=he513fc3_4
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.3.4=hed695b0_1
  • conda_env_yaml - Conda dep had pinned version number: conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1
  • conda_dockerfile - Found all expected strings in Dockerfile file
  • pipeline_name_conventions - Name adheres to nf-core convention
  • template_strings - Did not find any Jinja template strings (115 files)
  • schema_lint - Schema lint passed
  • schema_lint - Schema title + description lint passed
  • schema_params - Schema matched params returned from nextflow config
  • actions_schema_validation - Workflow validation passed: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
  • actions_schema_validation - Workflow validation passed: linting.yml
  • actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: ci.yml
  • merge_markers - No merge markers found in pipeline files

Run details

  • nf-core/tools version 1.14
  • Run at 2021-05-17 18:21:34

jfy133
jfy133 approved these changes May 17, 2021
View reviewed changes
Copy link
Member

@jfy133 jfy133 left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks simple enough, I assume failed tests are for other reasons

@maxulysse maxulysse merged commit 6ef72f0 into nf-core:dev May 17, 2021
@maxulysse
Copy link
Member Author

Yeah, I have some failure on the GATK spark tools that appeared when I upgraded the base image.
Not sure if I want to fix that, because it'll mean upgrading the gatk version, so not a minor release anymore...

@maxulysse maxulysse deleted the dev_json_fix branch August 4, 2021 12:45
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@jfy133 jfy133 jfy133 approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@maxulysse @jfy133