Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

jfy133 · 2022-10-24T09:25:21Z

I now remember why we had it in the first place 🙄

PR checklist

github-actions · 2022-10-24T09:25:31Z

This PR is against the `master` branch ❌

Do not close this PR
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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.
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Thanks again for your contribution!

jfy133 · 2022-10-24T09:26:41Z

@meganemichel and @aidaanva please try this branch -r patch-multivcfanalyzer-readgroups on your data both with and without running MultiVCFAnalyzer and check the VCF files look good (without MVA: include multiple samples in the VCF; with MVA: single samples in VCF so compatible with MVA)

github-actions · 2022-10-24T09:26:42Z

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

Posted for pipeline commit 415d05e

+| ✅ 386 tests passed       |+
#| ❔   5 tests were ignored |#
!| ❗  32 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conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.10.6 available
conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.3.4, 3.4.1 available
conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=8.2, 9.7 available
conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.9.0, 2.13.0 available
conda_env_yaml - Conda dep outdated: conda-forge::openjdk=8.0.144, 17.0.3 available
conda_env_yaml - Conda dep outdated: bioconda::adapterremoval=2.3.2, 2.3.3 available
conda_env_yaml - Conda dep outdated: bioconda::picard=2.26.0, 2.27.4 available
conda_env_yaml - Conda dep outdated: bioconda::samtools=1.12, 1.16.1 available
conda_env_yaml - Conda dep outdated: bioconda::angsd=0.935, 0.939 available
conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.2.0.0, 4.3.0.0 available
conda_env_yaml - Conda dep outdated: bioconda::gatk=3.5, 3.8 available
conda_env_yaml - Conda dep outdated: bioconda::damageprofiler=0.4.9, 1.1 available
conda_env_yaml - Conda dep outdated: bioconda::multiqc=1.13a, 1.13 available
conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.16, 1.17 available
conda_env_yaml - Conda dep outdated: bioconda::preseq=3.1.2, 3.2.0 available
conda_env_yaml - Conda dep outdated: bioconda::fastp=0.20.1, 0.23.2 available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, 1.5.1 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, 1.6.0 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, 39.01 available
conda_env_yaml - Conda dep outdated: bioconda::bcftools=1.12, 1.16 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:dev
nextflow_config - Config manifest.version ends in dev: '2.4.5dev'
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: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-2.4.5dev)
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
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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
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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
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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 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 dep had pinned version number: bioconda::fastp=0.20.1
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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
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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: push_dockerhub_dev.yml
actions_schema_validation - Workflow validation passed: awsfulltest.yml
actions_schema_validation - Workflow validation passed: ci.yml
actions_schema_validation - Workflow validation passed: linting.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: awstest.yml
merge_markers - No merge markers found in pipeline files

Run details

nf-core/tools version 1.14
Run at 2022-10-24 09:32:23

CHANGELOG.md

TCLamnidis · 2022-10-24T09:29:33Z

isnt the tool called AddOrReplaceReadGroups?

CHANGELOG.md

meganemichel · 2022-10-26T13:05:16Z

Tested patch and confirm that running with --run_multivcfanalyzer triggers updating of read groups, while running without --run_multivcfanalyzer produces unmodified vcfs.

apeltzer

Yes, 🥇

Re-add picard replacereadgroups for MVA only

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jfy133 changed the base branch from master to patch October 24, 2022 09:25

jfy133 commented Oct 24, 2022

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jfy133 requested a review from a team October 27, 2022 07:15

apeltzer approved these changes Oct 27, 2022

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jfy133 merged commit 9ea34fa into patch Oct 27, 2022

jfy133 deleted the patch-multivcfanalyzer-readgroups branch October 27, 2022 08:59

jfy133 mentioned this pull request Nov 11, 2022

Change read groups for genotyping when using MultiVCFAnalyzer #928

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Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

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Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

Re-add picard createorreplacereadgroups for MultiVCFanalyzer #930

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jfy133 commented Oct 24, 2022

PR checklist

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This PR is against the master branch ❌

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nf-core lint overall result: Passed ✅ ⚠️

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