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fix: tables for TSV files content #387

Merged
merged 2 commits into from
Jun 11, 2021
Merged

fix: tables for TSV files content #387

merged 2 commits into from
Jun 11, 2021

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maxulysse
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@FriederikeHanssen the info was actually there...

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).

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github-actions bot commented Jun 11, 2021 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit e54a778

+| ✅ 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  • conda_env_yaml - Conda dep outdated: conda-forge::llvm-openmp=8.0.1=hc9558a2_0, 11.1.0 available
  • conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1=py_0, 3.3.4 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0=py_0, 8.2 available
  • conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.5.2=py_0, 2.9.0 available
  • conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.9=ha228f0b_4, 1.12 available
  • conda_env_yaml - Conda dep outdated: bioconda::bwa-mem2=2.0=he513fc3_1, 2.2.1 available
  • conda_env_yaml - Conda dep outdated: bioconda::cancerit-allelecount=4.0.2=ha228f0b_1, 4.2.1 available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, 0.9.9 available
  • conda_env_yaml - Conda dep outdated: bioconda::ensembl-vep=99.2=pl526hecc5488_0, 104.3 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 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
  • 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
  • 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: ci.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: awsfulltest.yml
  • actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
  • actions_schema_validation - Workflow validation passed: awstest.yml
  • actions_schema_validation - Workflow validation passed: linting_comment.yml
  • actions_schema_validation - Workflow validation passed: branch.yml
  • merge_markers - No merge markers found in pipeline files

Run details

  • nf-core/tools version 1.14
  • Run at 2021-06-11 10:17:04

@FriederikeHanssen
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❤️ sneaky column format. LGTM!

@maxulysse maxulysse merged commit 6d8d3e4 into nf-core:dev Jun 11, 2021
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@maxulysse @FriederikeHanssen