Patch release 2.4.5

[jfy133]

[2.4.5] - 2022-07-39

Note: I've tweaked some of the DSL1 linting YML/files to make them work again so they've been added to the ignore stuff of the nf-core.yml.

Added

Fixed

• #882 Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian)
• #879 Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
• #880 Fix failure of endorSpy to be cached or reexecuted on resume (♥ to @KathrinNaegele, @TCLamnidis, & @mahesh-panchal for reporting and debugging)
• #885 Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
• #887 Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
• #889 Remove/updated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
• #895 Output documentation typo fix and added location of output docs in pipeline summary (♥ to @RodrigoBarquera for reporting)
• #897 Fix pipeline crash if no Kraken2 results generated (♥ to @alexandregilardet for reporting)
• #899 Fix pipeline crash for circulargenerator if reference file does not end in .fasta (♥ to @scarlhoff for reporting)
• Fixed some missing default values in the nextflow parameter schema JSON
• #789 Substantial speed and memory optimisation of the extract_map_reads.py script (♥ to @ivelsko for reporting, @maxibor for optimisation)
• Fix staging of input bams for genotyping_pileupcaller process. Downstream changes from changes introduced when fixing endorspy caching.

Dependencies

• Updated MultiQC to latest stable alpha version on bioconda, correcting the previously nonsensical AdapterRemoval plots (♥ to @NiemannJ for fixing in MultiQC)

Deprecated

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 274d8c0

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

Details

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: '2.4.5'
• 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• conda_env_yaml - Conda dep outdated: conda-forge::python=3.9.4, 3.10.5 available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, 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, 1.15.1 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:2.4.5
• 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:2.4.5
• 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:2.4.5
• 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-2.4.5)
• 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 2022-08-02 09:39:50

[TCLamnidis]

LGTM. I think the change in the tube maps is not in the CHANGELOG. not sure if it is needed?