Release PR for 2.3.5 patch

[jfy133]

Added

• #722 - Adds bwa -o flag for more flexibility in bwa parameters
• #736 - Add printing of multiqc run report location on successful completion
• New logo that is more visible when a user is using darkmode on GitHub or nf-core website!

Fixed

• #723 - Fixes empty fields in TSV resulting in uninformative error
• Updated template to nf-core/tools 1.14
• #688 - Clarified the pipeline is not just for humans and microbes, but also plants and animals, and also for modern DNA
• #751 - Added missing label to mtnucratio
• General code cleanup and standardisation of parameters with no default setting
• #750 - Fixed piped commands requesting the same number of CPUs at each command step
• #757 - Removed confusing 'Data Type' variable from MultiQC workflow summary (not consistent with TSV input)
• #759 - Fixed malformed software scraping regex that resulted in N/A in MultiQC report
• #761 - Fixed issues related to instability of samtools filtering related CI tests

Dependencies

Deprecated

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/eager branch on the nf-core/test-datasets repository.
• Make sure your code lints (nf-core lint .).
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Usage Documentation in docs/usage.md is updated.
• Output Documentation in docs/output.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

[github-actions]

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b54f41c

+| ✅ 365 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗  34 tests had warnings |!

❗ Test warnings:

• nextflow_config - Config manifest.version should end in dev: '2.3.5'
• 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• conda_env_yaml - Conda dep outdated: conda-forge::python=3.7.3, 3.9.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::markdown=3.2.2, 3.3.4 available
• conda_env_yaml - Conda dep outdated: conda-forge::pymdown-extensions=7.1, 8.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::pygments=2.6.1, 2.9.0 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::adapterremoval=2.3.1, 2.3.2 available
• conda_env_yaml - Conda dep outdated: bioconda::picard=2.22.9, 2.25.5 available
• conda_env_yaml - Conda dep outdated: bioconda::samtools=1.9, 1.12 available
• conda_env_yaml - Conda dep outdated: bioconda::angsd=0.933, 0.935 available
• conda_env_yaml - Conda dep outdated: bioconda::gatk4=4.1.7.0, 4.2.0.0 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::bedtools=2.29.2, 2.30.0 available
• conda_env_yaml - Conda dep outdated: conda-forge::libiconv=1.15, 1.16 available
• conda_env_yaml - Conda dep outdated: bioconda::preseq=2.0.3, 3.1.2 available
• conda_env_yaml - Conda dep outdated: bioconda::bamutil=1.0.14, 1.0.15 available
• conda_env_yaml - Conda dep outdated: bioconda::pysam=0.15.4, 0.16.0 available
• conda_env_yaml - Conda dep outdated: bioconda::kraken2=2.1.1, 2.1.2 available
• conda_env_yaml - Conda dep outdated: conda-forge::pandas=1.0.4, 1.2.4 available
• conda_env_yaml - Conda dep outdated: bioconda::freebayes=1.3.2, 1.3.5 available
• conda_env_yaml - Conda dep outdated: conda-forge::biopython=1.76, 1.78 available
• conda_env_yaml - Conda dep outdated: conda-forge::xopen=0.9.0, 1.1.0 available
• conda_env_yaml - Conda dep outdated: bioconda::bowtie2=2.4.2, 2.4.4 available
• conda_env_yaml - Conda dep outdated: bioconda::mapdamage2=2.2.0, 2.2.1 available
• conda_env_yaml - Conda dep outdated: bioconda::bbmap=38.87, 38.90 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:2.3.5
• 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_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:2.3.5
• 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:2.3.5
• 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-2.3.5)
• conda_env_yaml - Conda dep had pinned version number: conda-forge::python=3.7.3
• conda_env_yaml - Conda dep had pinned version number: conda-forge::markdown=3.2.2
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pymdown-extensions=7.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pygments=2.6.1
• 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=2.3.1
• 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=2.22.9
• conda_env_yaml - Conda dep had pinned version number: bioconda::samtools=1.9
• 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=0.933
• 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=4.1.7.0
• 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 package is the latest available: 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=2.29.2
• conda_env_yaml - Conda dep had pinned version number: conda-forge::libiconv=1.15
• 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=2.0.3
• 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=1.0.14
• 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=0.15.4
• conda_env_yaml - Conda dep had pinned version number: bioconda::kraken2=2.1.1
• conda_env_yaml - Conda dep had pinned version number: conda-forge::pandas=1.0.4
• conda_env_yaml - Conda dep had pinned version number: bioconda::freebayes=1.3.2
• 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=1.76
• conda_env_yaml - Conda dep had pinned version number: conda-forge::xopen=0.9.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bowtie2=2.4.2
• 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=2.2.0
• conda_env_yaml - Conda dep had pinned version number: bioconda::bbmap=38.87
• 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: ci.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_dev.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: awsfulltest.yml
• actions_schema_validation - Workflow validation passed: push_dockerhub_release.yml
• actions_schema_validation - Workflow validation passed: awstest.yml
• actions_schema_validation - Workflow validation passed: linting_comment.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 2021-06-03 09:11:36

[TCLamnidis]

See suggestions above

[jfy133]

One pass for each of both versions of nextflow, goo to enough for me (stupid samtools filter)