Codestin Search App

jfy133 · 2022-07-29T06:05:10Z

To get markdown/yml lint working, even if nf-core lint will continue to fail

Adds GHA fixes that were added by nf-core/core to template before the switch to prettier
Adds a YAML lint config file, to allow 'template' files to pass (otherwise nf-core linting would fail)
Fixes all the markdown linting errors accordingly

github-actions · 2022-07-29T06:05:24Z

This PR is against the `master` branch ❌

Do not close this PR
Click Edit and change the base to dev
This CI test will remain failed until you push a new commit

It looks like this pull-request is has been made against the nf-core/eager master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/eager dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

github-actions · 2022-07-29T06:05:35Z

YAML linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

Install yaml-lint
- Install npm then install yaml-lint (npm install -g yaml-lint)
Fix the markdown errors
- Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
- Fix any reported errors in your YAML files

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

github-actions · 2022-07-29T06:05:36Z

Markdown linting is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

Install markdownlint-cli
- On Mac: brew install markdownlint-cli
- Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
Fix the markdown errors
- Automatically: markdownlint . --config .github/markdownlint.yml --fix
- Manually resolve anything left from markdownlint . --config .github/markdownlint.yml

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!

This reverts commit f5f805c.

This reverts commit f6ebee3.

This reverts commit 99046cb.

github-actions · 2022-07-29T08:19:00Z

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

Posted for pipeline commit a81503b

+| ✅ 387 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  31 tests had warnings |!

Details

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: '2.4.4'
params_used - Config variable not found in main.nf: params.input_paths
params_used - Config variable not found in main.nf: params.enable_conda
conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.10.5 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.3.4, 3.4.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=8.2, 9.5 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.9.0, 2.12.0 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.15 available
conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.2, 2.3.3 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.26.0, 2.27.4 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.12, 1.15.1 available
conda_env_yaml - Conda dep outdated: bioconda::angsd=0.935, 0.939 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.2.0.0, 4.2.6.0 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.16, 1.17 available
conda_env_yaml - Conda dep outdated: bioconda::fastp=0.20.1, 0.23.2 available
conda_env_yaml - Conda dep outdated: bioconda::pysam=0.16.0, 0.19.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.2.4, 1.4.3 available
conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.5, 1.3.6 available
conda_env_yaml - Conda dep outdated: conda-forge::xopen=1.1.0, 1.5.0 available
conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.4.4, 2.4.5 available
conda_env_yaml - Conda dep outdated: bioconda::eigenstratdatabasetools=1.0.2, 1.1.0 available
conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.92, 38.97 available
conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.12, 1.15.1 available
schema_description - No description provided in schema for parameter: skip_fastqc
schema_description - No description provided in schema for parameter: skip_adapterremoval
schema_description - No description provided in schema for parameter: skip_preseq
schema_description - No description provided in schema for parameter: skip_deduplication
schema_description - No description provided in schema for parameter: skip_damage_calculation
schema_description - No description provided in schema for parameter: skip_qualimap

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.md
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: docs/README.md
files_unchanged - File ignored due to lint config: assets/multiqc_config.yaml

✅ 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-eager_logo.png
files_exist - File found: bin/markdown_to_html.py
files_exist - File found: docs/images/nf-core-eager_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/eager:2.4.4
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.genome
params_used - Config variable found in main.nf: params.input
params_used - Config variable found in main.nf: params.single_end
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.awsqueue
params_used - Config variable found in main.nf: params.awsregion
params_used - Config variable found in main.nf: params.awscli
params_used - Config variable found in main.nf: params.validate_params
params_used - Config variable found in main.nf: params.udg_type
params_used - Config variable found in main.nf: params.single_stranded
params_used - Config variable found in main.nf: params.colour_chemistry
params_used - Config variable found in main.nf: params.bam
params_used - Config variable found in main.nf: params.snpcapture_bed
params_used - Config variable found in main.nf: params.run_convertinputbam
params_used - Config variable found in main.nf: params.fasta
params_used - Config variable found in main.nf: params.bwa_index
params_used - Config variable found in main.nf: params.bt2_index
params_used - Config variable found in main.nf: params.fasta_index
params_used - Config variable found in main.nf: params.seq_dict
params_used - Config variable found in main.nf: params.large_ref
params_used - Config variable found in main.nf: params.save_reference
params_used - Config variable found in main.nf: params.genomes
params_used - Config variable found in main.nf: params.skip_fastqc
params_used - Config variable found in main.nf: params.skip_adapterremoval
params_used - Config variable found in main.nf: params.skip_preseq
params_used - Config variable found in main.nf: params.skip_deduplication
params_used - Config variable found in main.nf: params.skip_damage_calculation
params_used - Config variable found in main.nf: params.skip_qualimap
params_used - Config variable found in main.nf: params.complexity_filter_poly_g
params_used - Config variable found in main.nf: params.complexity_filter_poly_g_min
params_used - Config variable found in main.nf: params.clip_forward_adaptor
params_used - Config variable found in main.nf: params.clip_reverse_adaptor
params_used - Config variable found in main.nf: params.clip_adapters_list
params_used - Config variable found in main.nf: params.clip_readlength
params_used - Config variable found in main.nf: params.clip_min_read_quality
params_used - Config variable found in main.nf: params.min_adap_overlap
params_used - Config variable found in main.nf: params.skip_collapse
params_used - Config variable found in main.nf: params.skip_trim
params_used - Config variable found in main.nf: params.preserve5p
params_used - Config variable found in main.nf: params.mergedonly
params_used - Config variable found in main.nf: params.qualitymax
params_used - Config variable found in main.nf: params.run_post_ar_trimming
params_used - Config variable found in main.nf: params.post_ar_trim_front
params_used - Config variable found in main.nf: params.post_ar_trim_tail
params_used - Config variable found in main.nf: params.post_ar_trim_front2
params_used - Config variable found in main.nf: params.post_ar_trim_tail2
params_used - Config variable found in main.nf: params.mapper
params_used - Config variable found in main.nf: params.bwaalnn
params_used - Config variable found in main.nf: params.bwaalnk
params_used - Config variable found in main.nf: params.bwaalnl
params_used - Config variable found in main.nf: params.bwaalno
params_used - Config variable found in main.nf: params.circularextension
params_used - Config variable found in main.nf: params.circulartarget
params_used - Config variable found in main.nf: params.circularfilter
params_used - Config variable found in main.nf: params.bt2_alignmode
params_used - Config variable found in main.nf: params.bt2_sensitivity
params_used - Config variable found in main.nf: params.bt2n
params_used - Config variable found in main.nf: params.bt2l
params_used - Config variable found in main.nf: params.bt2_trim5
params_used - Config variable found in main.nf: params.bt2_trim3
params_used - Config variable found in main.nf: params.bt2_maxins
params_used - Config variable found in main.nf: params.hostremoval_input_fastq
params_used - Config variable found in main.nf: params.hostremoval_mode
params_used - Config variable found in main.nf: params.run_bam_filtering
params_used - Config variable found in main.nf: params.bam_mapping_quality_threshold
params_used - Config variable found in main.nf: params.bam_filter_minreadlength
params_used - Config variable found in main.nf: params.bam_unmapped_type
params_used - Config variable found in main.nf: params.dedupper
params_used - Config variable found in main.nf: params.dedup_all_merged
params_used - Config variable found in main.nf: params.preseq_step_size
params_used - Config variable found in main.nf: params.preseq_mode
params_used - Config variable found in main.nf: params.preseq_bootstrap
params_used - Config variable found in main.nf: params.preseq_maxextrap
params_used - Config variable found in main.nf: params.preseq_cval
params_used - Config variable found in main.nf: params.preseq_terms
params_used - Config variable found in main.nf: params.damageprofiler_length
params_used - Config variable found in main.nf: params.damageprofiler_threshold
params_used - Config variable found in main.nf: params.damageprofiler_yaxis
params_used - Config variable found in main.nf: params.run_pmdtools
params_used - Config variable found in main.nf: params.pmdtools_range
params_used - Config variable found in main.nf: params.pmdtools_threshold
params_used - Config variable found in main.nf: params.pmdtools_reference_mask
params_used - Config variable found in main.nf: params.pmdtools_max_reads
params_used - Config variable found in main.nf: params.pmdtools_platypus
params_used - Config variable found in main.nf: params.run_mapdamage_rescaling
params_used - Config variable found in main.nf: params.rescale_length_5p
params_used - Config variable found in main.nf: params.rescale_length_3p
params_used - Config variable found in main.nf: params.run_bedtools_coverage
params_used - Config variable found in main.nf: params.anno_file
params_used - Config variable found in main.nf: params.run_trim_bam
params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_half_udg_right
params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_double_stranded_none_udg_right
params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_half_udg_right
params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_single_stranded_none_udg_right
params_used - Config variable found in main.nf: params.bamutils_softclip
params_used - Config variable found in main.nf: params.run_genotyping
params_used - Config variable found in main.nf: params.genotyping_tool
params_used - Config variable found in main.nf: params.genotyping_source
params_used - Config variable found in main.nf: params.gatk_call_conf
params_used - Config variable found in main.nf: params.gatk_ploidy
params_used - Config variable found in main.nf: params.gatk_downsample
params_used - Config variable found in main.nf: params.gatk_dbsnp
params_used - Config variable found in main.nf: params.gatk_hc_out_mode
params_used - Config variable found in main.nf: params.gatk_hc_emitrefconf
params_used - Config variable found in main.nf: params.gatk_ug_genotype_model
params_used - Config variable found in main.nf: params.gatk_ug_out_mode
params_used - Config variable found in main.nf: params.gatk_ug_keep_realign_bam
params_used - Config variable found in main.nf: params.gatk_ug_defaultbasequalities
params_used - Config variable found in main.nf: params.freebayes_C
params_used - Config variable found in main.nf: params.freebayes_g
params_used - Config variable found in main.nf: params.freebayes_p
params_used - Config variable found in main.nf: params.pileupcaller_snpfile
params_used - Config variable found in main.nf: params.pileupcaller_bedfile
params_used - Config variable found in main.nf: params.pileupcaller_method
params_used - Config variable found in main.nf: params.pileupcaller_transitions_mode
params_used - Config variable found in main.nf: params.pileupcaller_min_map_quality
params_used - Config variable found in main.nf: params.pileupcaller_min_base_quality
params_used - Config variable found in main.nf: params.angsd_glmodel
params_used - Config variable found in main.nf: params.angsd_glformat
params_used - Config variable found in main.nf: params.angsd_createfasta
params_used - Config variable found in main.nf: params.angsd_fastamethod
params_used - Config variable found in main.nf: params.run_bcftools_stats
params_used - Config variable found in main.nf: params.run_vcf2genome
params_used - Config variable found in main.nf: params.vcf2genome_outfile
params_used - Config variable found in main.nf: params.vcf2genome_header
params_used - Config variable found in main.nf: params.vcf2genome_minc
params_used - Config variable found in main.nf: params.vcf2genome_minq
params_used - Config variable found in main.nf: params.vcf2genome_minfreq
params_used - Config variable found in main.nf: params.run_multivcfanalyzer
params_used - Config variable found in main.nf: params.write_allele_frequencies
params_used - Config variable found in main.nf: params.min_genotype_quality
params_used - Config variable found in main.nf: params.min_base_coverage
params_used - Config variable found in main.nf: params.min_allele_freq_hom
params_used - Config variable found in main.nf: params.min_allele_freq_het
params_used - Config variable found in main.nf: params.additional_vcf_files
params_used - Config variable found in main.nf: params.reference_gff_annotations
params_used - Config variable found in main.nf: params.reference_gff_exclude
params_used - Config variable found in main.nf: params.snp_eff_results
params_used - Config variable found in main.nf: params.run_mtnucratio
params_used - Config variable found in main.nf: params.mtnucratio_header
params_used - Config variable found in main.nf: params.run_sexdeterrmine
params_used - Config variable found in main.nf: params.sexdeterrmine_bedfile
params_used - Config variable found in main.nf: params.run_nuclear_contamination
params_used - Config variable found in main.nf: params.contamination_chrom_name
params_used - Config variable found in main.nf: params.run_metagenomic_screening
params_used - Config variable found in main.nf: params.metagenomic_complexity_filter
params_used - Config variable found in main.nf: params.metagenomic_complexity_entropy
params_used - Config variable found in main.nf: params.metagenomic_tool
params_used - Config variable found in main.nf: params.database
params_used - Config variable found in main.nf: params.metagenomic_min_support_reads
params_used - Config variable found in main.nf: params.percent_identity
params_used - Config variable found in main.nf: params.malt_mode
params_used - Config variable found in main.nf: params.malt_alignment_mode
params_used - Config variable found in main.nf: params.malt_top_percent
params_used - Config variable found in main.nf: params.malt_min_support_mode
params_used - Config variable found in main.nf: params.malt_min_support_percent
params_used - Config variable found in main.nf: params.malt_max_queries
params_used - Config variable found in main.nf: params.malt_memory_mode
params_used - Config variable found in main.nf: params.malt_sam_output
params_used - Config variable found in main.nf: params.run_maltextract
params_used - Config variable found in main.nf: params.maltextract_taxon_list
params_used - Config variable found in main.nf: params.maltextract_ncbifiles
params_used - Config variable found in main.nf: params.maltextract_filter
params_used - Config variable found in main.nf: params.maltextract_toppercent
params_used - Config variable found in main.nf: params.maltextract_destackingoff
params_used - Config variable found in main.nf: params.maltextract_downsamplingoff
params_used - Config variable found in main.nf: params.maltextract_duplicateremovaloff
params_used - Config variable found in main.nf: params.maltextract_matches
params_used - Config variable found in main.nf: params.maltextract_megansummary
params_used - Config variable found in main.nf: params.maltextract_percentidentity
params_used - Config variable found in main.nf: params.maltextract_topalignment
params_used - Config variable found in main.nf: params.multiqc_config
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.max_multiqc_email_size
params_used - Config variable found in main.nf: params.plaintext_email
params_used - Config variable found in main.nf: params.monochrome_logs
params_used - Config variable found in main.nf: params.help
params_used - Config variable found in main.nf: params.tracedir
params_used - Config variable found in main.nf: params.hostnames
params_used - Config variable found in main.nf: params.config_profile_description
params_used - Config variable found in main.nf: params.config_profile_contact
params_used - Config variable found in main.nf: params.config_profile_url
params_used - Config variable found in main.nf: params.max_memory
params_used - Config variable found in main.nf: params.max_cpus
params_used - Config variable found in main.nf: params.max_time
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/ISSUE_TEMPLATE/config.yml matches the template
files_unchanged - .github/ISSUE_TEMPLATE/feature_request.md matches the template
files_unchanged - .github/markdownlint.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 - 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 - assets/nf-core-eager_logo.png matches the template
files_unchanged - bin/markdown_to_html.py matches the template
files_unchanged - docs/images/nf-core-eager_logo.png 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
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/eager:2.4.4
actions_ci - CI is pulling the correct docker image: docker pull nfcore/eager:dev
actions_ci - CI is tagging docker image correctly: docker tag nfcore/eager:dev nfcore/eager:2.4.4
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
actions_awsfulltest - .github/workflows/awsfulltest.yml does not use -profile test
readme - README Nextflow minimum version badge matched config. Badge: 20.07.1, Config: 20.07.1
readme - README had a bioconda badge
conda_env_yaml - Conda environment name was correct (nf-core-eager-2.4.4)
conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.9.4
conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.3.4
conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=8.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.9.0
conda_env_yaml - Conda dep had pinned version number: bioconda::rename=1.601
conda_env_yaml - Conda package is the latest available: bioconda::rename=1.601
conda_env_yaml - Conda dep had pinned version number: conda-forge::openjdk=8.0.144
conda_env_yaml - Conda dep had pinned version number: bioconda::fastqc=0.11.9
conda_env_yaml - Conda package is the latest available: bioconda::fastqc=0.11.9
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremoval=2.3.2
conda_env_yaml - Conda dep had pinned version number: bioconda::adapterremovalfixprefix=0.0.5
conda_env_yaml - Conda package is the latest available: bioconda::adapterremovalfixprefix=0.0.5
conda_env_yaml - Conda dep had pinned version number: bioconda::bwa=0.7.17
conda_env_yaml - Conda package is the latest available: bioconda::bwa=0.7.17
conda_env_yaml - Conda dep had pinned version number: bioconda::picard=2.26.0
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
conda_env_yaml - Conda dep had pinned version number: bioconda::dedup=0.12.8
conda_env_yaml - Conda package is the latest available: bioconda::dedup=0.12.8
conda_env_yaml - Conda dep had pinned version number: bioconda::angsd=0.935
conda_env_yaml - Conda dep had pinned version number: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda package is the latest available: bioconda::circularmapper=1.93.5
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk4=4.2.0.0
conda_env_yaml - Conda dep had pinned version number: bioconda::gatk=3.5
conda_env_yaml - Conda dep had pinned version number: bioconda::qualimap=2.2.2d
conda_env_yaml - Conda package is the latest available: bioconda::qualimap=2.2.2d
conda_env_yaml - Conda dep had pinned version number: bioconda::vcf2genome=0.91
conda_env_yaml - Conda package is the latest available: bioconda::vcf2genome=0.91
conda_env_yaml - Conda dep had pinned version number: bioconda::damageprofiler=0.4.9
conda_env_yaml - Conda dep had pinned version number: bioconda::multiqc=1.13a
conda_env_yaml - Conda package is the latest available: bioconda::multiqc=1.13a
conda_env_yaml - Conda dep had pinned version number: bioconda::pmdtools=0.60
conda_env_yaml - Conda package is the latest available: bioconda::pmdtools=0.60
conda_env_yaml - Conda dep had pinned version number: bioconda::bedtools=2.30.0
conda_env_yaml - Conda package is the latest available: bioconda::bedtools=2.30.0
conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.16
conda_env_yaml - Conda dep had pinned version number: conda-forge::pigz=2.6
conda_env_yaml - Conda package is the latest available: conda-forge::pigz=2.6
conda_env_yaml - Conda dep had pinned version number: bioconda::sequencetools=1.5.2
conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.5.2
conda_env_yaml - Conda dep had pinned version number: bioconda::preseq=3.1.2
conda_env_yaml - Conda package is the latest available: bioconda::preseq=3.1.2
conda_env_yaml - Conda dep had pinned version number: bioconda::fastp=0.20.1
conda_env_yaml - Conda dep had pinned version number: bioconda::bamutil=1.0.15
conda_env_yaml - Conda package is the latest available: bioconda::bamutil=1.0.15
conda_env_yaml - Conda dep had pinned version number: bioconda::mtnucratio=0.7
conda_env_yaml - Conda package is the latest available: bioconda::mtnucratio=0.7
conda_env_yaml - Conda dep had pinned version number: bioconda::pysam=0.16.0
conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.2
conda_env_yaml - Conda package is the latest available: bioconda::kraken2=2.1.2
conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.2.4
conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.5
conda_env_yaml - Conda dep had pinned version number: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda package is the latest available: bioconda::sexdeterrmine=1.1.2
conda_env_yaml - Conda dep had pinned version number: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda package is the latest available: bioconda::multivcfanalyzer=0.85.2
conda_env_yaml - Conda dep had pinned version number: bioconda::hops=0.35
conda_env_yaml - Conda package is the latest available: bioconda::hops=0.35
conda_env_yaml - Conda dep had pinned version number: conda-forge::biopython=1.79
conda_env_yaml - Conda package is the latest available: conda-forge::biopython=1.79
conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=1.1.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.4
conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda dep had pinned version number: bioconda::mapdamage2=2.2.1
conda_env_yaml - Conda package is the latest available: bioconda::mapdamage2=2.2.1
conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.92
conda_env_yaml - Conda dep had pinned version number: bioconda::bcftools=1.12
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 (151 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: linting.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: awstest.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.14
Run at 2022-07-29 08:18:41

TCLamnidis

LGTM

Pin to later version of node as in nf-core/tools#1398

199a02b

jfy133 changed the base branch from master to dev July 29, 2022 06:05

jfy133 added 2 commits July 29, 2022 08:06

Update linting.yml

2997adc

Update .nf-core-lint.yml

c6ea117

jfy133 marked this pull request as draft July 29, 2022 06:11

jfy133 added 12 commits July 29, 2022 08:13

prettier fixes

99046cb

Fix markdown linting

f6ebee3

Revert nf-core non-standard linting files but still template

f5f805c

Revert "Revert nf-core non-standard linting files but still template"

cedb950

This reverts commit f5f805c.

Revert "Fix markdown linting"

0a0b4b3

This reverts commit f6ebee3.

Revert "prettier fixes"

687eb7f

This reverts commit 99046cb.

Fix markdown linting

391489a

Final markdown linting

2ac8389

Fix inconssitency with template

260d780

Missing new line

0d7fbbf

Try custom yaml linting

9b9173d

fix yaml lint config param

a81503b

jfy133 marked this pull request as ready for review July 29, 2022 08:26

jfy133 requested a review from TCLamnidis July 29, 2022 08:52

TCLamnidis approved these changes Jul 29, 2022

View reviewed changes

jfy133 merged commit f1e6be9 into dev Jul 29, 2022

jfy133 deleted the linting-fixes branch July 29, 2022 11:02

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Linting fixes#910

Linting fixes#910
jfy133 merged 15 commits intodevfrom
linting-fixes

jfy133 commented Jul 29, 2022 •

edited

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github-actions bot commented Jul 29, 2022 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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jfy133 commented Jul 29, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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github-actions bot commented Jul 29, 2022

This PR is against the master branch ❌

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github-actions bot commented Jul 29, 2022

YAML linting is failing

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github-actions bot commented Jul 29, 2022

Markdown linting is failing

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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jfy133 commented Jul 29, 2022 •

edited

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This PR is against the `master` branch ❌

github-actions bot commented Jul 29, 2022 •

edited

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