Dev sync 1.14 #373

maxulysse · 2021-05-12T12:27:47Z

PR checklist

github-actions · 2021-05-13T09:21:13Z

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

Posted for pipeline commit b007809

+| ✅ 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conda_env_yaml - Conda dep outdated: conda-forge::llvm-openmp=8.0.1=hc9558a2_0, 11.1.0 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.1.1=py_0, 3.3.4 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=6.0=py_0, 8.2 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.5.2=py_0, 2.9.0 available
conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.9=ha228f0b_4, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::bwa-mem2=2.0=he513fc3_1, 2.2.1 available
conda_env_yaml - Conda dep outdated: bioconda::cancerit-allelecount=4.0.2=ha228f0b_1, 4.2.1 available
conda_env_yaml - Conda dep outdated: bioconda::cnvkit=0.9.6=py27_1, 0.9.8 available
conda_env_yaml - Conda dep outdated: bioconda::ensembl-vep=99.2=pl526hecc5488_0, 104.0 available
conda_env_yaml - Conda dep outdated: bioconda::fgbio=1.1.0=0, 1.3.0 available
conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2=py27h49fb759_2, 1.3.5 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4-spark=4.1.7.0=0, 4.2.0.0 available
conda_env_yaml - Conda dep outdated: bioconda::htslib=1.9=ha228f0b_7, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.8=py_2, 1.10.1 available
conda_env_yaml - Conda dep outdated: bioconda::samblaster=0.1.24=hc9558a2_3, 0.1.26 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9=h10a08f8_12, 1.12 available
conda_env_yaml - Conda dep outdated: bioconda::snpeff=4.3.1t=0, 5.0 available
conda_env_yaml - Conda dep outdated: bioconda::tiddit=2.7.1=py27hb3f55d8_1, 2.12.1 available
conda_env_yaml - Conda dep outdated: bioconda::trim-galore=0.6.5=0, 0.6.6 available
conda_env_yaml - Conda dep outdated: conda-forge::pigz=2.3.4=hed695b0_1, 2.6 available
conda_env_yaml - Conda dep outdated: conda-forge::r-ggplot2=3.3.0=r40h6115d3f_1, 3.3.3 available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 2021-05-13 10:04:32

nservant

Looks good to me

nf-core-bot and others added 16 commits March 18, 2021 12:05

Template update for nf-core/tools version 1.13

8ff0c14

Template update for nf-core/tools version 1.13.1

86e3c46

Template update for nf-core/tools version 1.13.2

ca1d60a

Template update for nf-core/tools version 1.13.3

c8721a7

Template update for nf-core/tools version 1.14

5cc5c52

Merge remote-tracking branch 'upstream/TEMPLATE' into dev_sync_1.14

e8c6c6f

fix: forgot to resolve conflicts here

93a3d72

fix: schema fixed + remove warnings

70e5f07

fix: markdownlint

e9f58ee

fix: nf-core lint dag error

a3c6d28

fix: link to docs

7bc1c4a

fix: more lint

2e280b6

fix: more nf-core lint

2df52b0

fix: more nf-core lint

fb4f64e

fix: update files

58f58dc

fix: nf-core lint works

af57fab

maxulysse added 8 commits May 13, 2021 11:27

fix: schema

f7f0b6e

fix: json schema

991dc0f

fix: enum -> list in schema for --tools

01ed8b4

fix: typo

acb7ba8

fix: typo

d90fa01

feat: ASCII art is back

7fe9087

fix: nf-core lint

6ca7650

fix: schema

b007809

nservant approved these changes May 13, 2021

View reviewed changes

maxulysse merged commit 5e27b2e into nf-core:dev May 13, 2021

maxulysse deleted the dev_sync_1.14 branch May 13, 2021 14:26

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Dev sync 1.14 #373

Dev sync 1.14 #373

maxulysse commented May 12, 2021

github-actions bot commented May 13, 2021 •

edited

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

nservant left a comment

Dev sync 1.14 #373

Dev sync 1.14 #373

Conversation

maxulysse commented May 12, 2021

PR checklist

github-actions bot commented May 13, 2021 • edited

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

nservant left a comment

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github-actions bot commented May 13, 2021 •

edited

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