Major release wangen #767

jfy133 · 2021-06-07T12:50:43Z

This will include updated tool versions and new functionality not just patches.

Will likely be last one before DSL2 and eager3

Important Need to update the figures/diagrams BEFORE MERGING with @ZandraFagernas, however will wait until everything is in first.
Important Need to make DEPENDENCIES (i.e .conda version bumps) list in CHANGELOG

PR checklist

Get latest dev into bcftools branch

Get upstream fixes for tests to pass

Get latest dev into wangen base

github-actions · 2021-06-07T12:53:14Z

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

Posted for pipeline commit 15d3b7e

+| ✅ 384 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  15 tests had warnings |!

Details

❗ Test warnings:

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conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.9.5 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 11.0.9.1 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.25.5, 2.25.6 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.10.1, 1.11 available
conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.2.4, 1.3.0 available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: 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:dev
nextflow_config - Config manifest.version ends in dev: '2.4dev'
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_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.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.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_half_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_half_udg_right
params_used - Config variable found in main.nf: params.bamutils_clip_none_udg_left
params_used - Config variable found in main.nf: params.bamutils_clip_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.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_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 - .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 - 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:dev
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: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
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-2.4dev)
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 package is the latest available: 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 package is the latest available: 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 package is the latest available: 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 package is the latest available: 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=2.25.5
conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.12
conda_env_yaml - Conda package is the latest available: 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 package is the latest available: 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 package is the latest available: 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=1.10.1
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 package is the latest available: 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=1.4.0.6
conda_env_yaml - Conda package is the latest available: bioconda::sequencetools=1.4.0.6
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 package is the latest available: 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 package is the latest available: 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 package is the latest available: 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 package is the latest available: conda-forge::xopen=1.1.0
conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.4
conda_env_yaml - Conda package is the latest available: bioconda::bowtie2=2.4.4
conda_env_yaml - Conda dep had pinned version number: bioconda::eigenstratdatabasetools=1.0.2
conda_env_yaml - Conda package is the latest available: 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=38.90
conda_env_yaml - Conda package is the latest available: bioconda::bbmap=38.90
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 (148 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: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.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: ci.yml
actions_schema_validation - Workflow validation passed: push_dockerhub_release.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 2021-07-06 07:21:52

Improve BoeTiw2 output documentation

Add AR adapterList removal

@robert-davidson

Add LC_Extrap mode for @robert-davidson

Add basic functionality for barcode trimming/fastq trimming

Co-authored-by: Alexander Peltzer <[email protected]>

Add Bcftools stats and change VCF compression

Update best practise defults and bam trimming defaults

Info bump

apeltzer

Reviewed most of this anyways before so 🤷🏻 😆 🤠

jfy133 added 18 commits April 30, 2021 14:23

Add bcftools stats modules

66d4a68

Add bcftools - still missing output docs

51f5790

Remove unnecessary branching

56a50bc

Add docs and fix compatibility with MVA and VCF2Genomes

f9bc10a

Update output.md

e0fae4e

Remove now uncessary CONTRIBUTING step due to new magic groovy functions

9032bf6

Merge branch 'bcftools' of github.com:nf-core/eager into bcftools

148631d

Software version reporting fixes and additions

3702a07

Update changelog

a47f744

Update CHANGELOG.md

d92bcf2

Merge branch 'major-release-wangen' into bcftools

f2f4ce7

Merge branch 'bcftools' into dev-for-bcftools

5cf6af5

Merge pull request #749 from nf-core/dev-for-bcftools

110d47e

Get latest dev into bcftools branch

Merge pull request #752 from nf-core/validation-fixes-patch

429e311

Get upstream fixes for tests to pass

Merge pull request #756 from nf-core/dev

18b49c9

Get latest dev into wangen base

Add basic functionality for barcode trimming -

a48953e

Add CI tests

5ed9de6

Bump pipeline and tool versions

0b5d95a

jfy133 marked this pull request as draft June 7, 2021 12:50

Merge branch 'dev' into major-release-wangen

8d80552

jfy133 added 9 commits June 7, 2021 15:33

dd additional CI

bdfc5a1

Merge branch 'major-release-wangen' into bcftools

6876e81

Bump vcftools verison to latest

a9f18d3

Fix script

ea7f905

Fix naming conflict when skip AR + running post_ar trim

231ae78

Add AR adapterList removal

342ec92

mardown lint

d95f31c

Input channel in input and not output :grimace:

6807e5c

Update CHANGELOG.md

61c1d7f

jfy133 and others added 17 commits August 11, 2021 15:34

Update CHANGELOG.md

230aed6

Merge pull request #782 from nf-core/docs-update

5ccc1c3

Improve BoeTiw2 output documentation

Merge pull request #768 from nf-core/adapter-list

c0c2997

Add AR adapterList removal

Merge branch 'major-release-wangen' into preseq-extension

ff3cef3

Merge pull request #780 from nf-core/preseq-extension

b057f0a

Add LC_Extrap mode for @robert-davidson

Merge branch 'major-release-wangen' into inline-barcode-trimming

e02bc14

Update contributors list

54396a8

Merge pull request #765 from nf-core/inline-barcode-trimming

2519dcb

Add basic functionality for barcode trimming/fastq trimming

Update docs/output.md

a68b9d4

Co-authored-by: Alexander Peltzer <[email protected]>

Delete useless block

d51783e

Update best practise defults and bam trimming defaults

91c51f4

Merge branch 'major-release-wangen' into bcftools

66b1bc6

Changelog linting

1d42a5c

A few version bumps

5ce424a

Sync bcftools with samtools version

93da6ea

Merge pull request #737 from nf-core/bcftools

31df912

Add Bcftools stats and change VCF compression

Merge pull request #784 from nf-core/defaults-update

c12c9e6

Update best practise defults and bam trimming defaults

jfy133 marked this pull request as ready for review August 24, 2021 09:35

jfy133 added 6 commits August 24, 2021 20:26

Update CHANGELOG to report all updateed dependencies

55317f3

Update images for release

8e81bd3

Update CHANGELOG.md

0564e16

Tweaks

fede5a4

Merge branch 'info-bump' of github.com:nf-core/eager into info-bump

b2bf363

Merge pull request #785 from nf-core/info-bump

720580b

Info bump

jfy133 changed the title ~~[PseudoPR] Major release wangen~~ Major release wangen Aug 26, 2021

jfy133 requested review from a team and apeltzer August 26, 2021 07:36

apeltzer approved these changes Aug 26, 2021

View reviewed changes

jfy133 merged commit 76d048b into dev Aug 26, 2021

jfy133 deleted the major-release-wangen branch September 15, 2021 12:09

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Major release wangen #767

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nf-core lint overall result: Passed ✅ ⚠️

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jfy133 commented Jun 7, 2021 •

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