Dev

[mattheww95]

No description provided.

[github-actions]

nf-core lint overall result: Failed ❌

Posted for pipeline commit 4073f67

+| ✅ 108 tests passed       |+
#| ❔  18 tests were ignored |#
!| ❗ 886 tests had warnings |!
-| ❌ 450 tests failed       |-

❌ Test failures:

• files_exist - File not found: .gitattributes
• files_exist - File not found: .editorconfig
• files_exist - File not found: .github/workflows/branch.yml
• files_exist - File not found: docs/output.md
• files_exist - File not found: docs/README.md
• files_exist - File not found: docs/README.md
• files_exist - File not found: docs/usage.md
• files_unchanged - LICENSE does not match the template
• files_unchanged - .github/CONTRIBUTING.md does not match the template
• files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
• files_unchanged - .github/ISSUE_TEMPLATE/feature_request.yml does not match the template
• files_unchanged - .github/PULL_REQUEST_TEMPLATE.md does not match the template
• files_unchanged - .github/workflows/linting_comment.yml does not match the template
• files_unchanged - assets/email_template.html does not match the template
• files_unchanged - assets/email_template.txt does not match the template
• files_unchanged - assets/sendmail_template.txt does not match the template
• files_unchanged - lib/NfcoreSchema.groovy does not match the template
• files_unchanged - .gitignore does not match the template
• actions_ci - '.github/workflows/ci.yml' is not triggered on expected events
• actions_ci - '.github/workflows/ci.yml' does not check minimum NF version
• schema_params - Default value for param coreutils.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param samtools.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param racon.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bandage.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kleborate.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param lissero.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param python3.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param abricate.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param coreutils.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param chopper.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param samtools.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param racon.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bandage.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kleborate.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param lissero.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param python3.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param abricate.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.db invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.txt_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.xlsx_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.point_finder_dbs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param staramr.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.singularity invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.docker invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.results_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.mob_results_file invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.contig_report invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mobsuite_recon.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param slurm_profile invalid: String should not be set to ''
• schema_params - Default value for param kat.hist_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.png_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.postscript_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.output_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.pdf_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kat.jfhash_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param opt_platforms.ont invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param opt_platforms.pacbio invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param opt_platforms.hybrid invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param opt_platforms.illumina invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.seed invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.reads_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.html_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.average_quality_e invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.cut_mean_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.qualified_quality_phred invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.unqualified_percent_limit invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.fastq_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.illumina_length_min invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.single_end_length_min invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.dedup_reads invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.args.illumina invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.args.single_end invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.nanopore.corr invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.nanopore.hq invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.pacbio.raw invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.pacbio.corr invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.nanopore.raw invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.gfa_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.gv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.txt_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.log_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.polishing_iterations invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.pacbio.hq invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param flye.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.report_base invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.report_prefix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.report_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast_filter.n50_field invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast_filter.n50_value invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast_filter.nr_contigs_field invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast_filter.nr_contigs_value invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast_filter.sample_header invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.min_contig_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.scaffolds_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.contigs_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.transcripts_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.gene_clusters_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.assembly_graphs_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.log_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spades.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.alignment_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.results_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.folder_name invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.gzip_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.lineage_ms invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.db invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.classified_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.unclassified_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.report_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.output_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.save_output_fastqs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.save_reads_assignments invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.run_kraken_quick invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.tophit_level invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken_bin.taxonomic_level invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param chopper.quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param chopper.minlength invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param chopper.fastq_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastqc.html_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastqc.zip_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.mash_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.output_reads_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.output_taxa_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.output_dir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.mash_sketch invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.sketch_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.sketch_kmer_size invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.final_sketch_name invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.phix_fa invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.homo_sapiens_fa invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.pacbio_mg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.output_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.mega_mm2_idx invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.mm2_illumina invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.mm2_pac invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.mm2_ont invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.mm2_output_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.samtools_output_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.samtools_singletons_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.samtools_output_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param r_contaminants.output_dir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.index_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.index_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.mapped_paf_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.mapped_sam_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param minimap2.mapped_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param samtools.bam_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param samtools.bai_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param racon.consensus_suffix invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param racon.consensus_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param racon.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.fasta_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.vcf_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.vcf_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.changes_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.changes_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon.max_memory_multiplier invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.fasta_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.vcf_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.vcf_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.bam_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.bai_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.changes_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.changes_outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.max_memory_multiplier invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.max_polishing_illumina invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.max_polishing_pacbio invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pilon_iterative.max_polishing_nanopore invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.model invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param medaka.batch_size invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.scaffolds_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.assembly_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.log_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.mem_modifier invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param unicycler.threads_increase_factor invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.output_dir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.embl_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.faa_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.ffn_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.fna_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.gbff_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.gff_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.threads invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.hypotheticals_tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.hypotheticals_faa_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.txt_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.min_contig_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bandage.svg_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bandage.outdir invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.log_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.txt_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.allele_fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.allele_json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.cgmlst_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param lissero.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param lissero.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param raw_reads.high_precision invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param raw_reads.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.assembly_fastq invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param seqtk.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param fastp.report_exclude_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param quast.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param checkm.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken.headers invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mlst.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.json_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.min_kmer invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash.headers invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param mash_meta.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param top_hit_species.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken_species.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param subtyping_report.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param ectyper.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kleborate.txt_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kleborate.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kleborate.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.tsv_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.repeats invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param spatyper.repeat_order invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param sistr.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param lissero.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param kraken_bin.fasta_ext invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.escherichia.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.salmonella.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.shigella.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.listeria.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.campylobacter.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.vibrio.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.klebsiella.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.staphylococcus.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.search invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.raw_average_quality invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.min_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.max_n50 invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.min_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.max_nr_contigs invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.min_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.max_length invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.max_checkm_contamination invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReport.fallthrough.min_average_coverage invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.raw_average_quality.low_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.average_coverage.low_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.metagenomic.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.metagenomic.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.metagenomic.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.metagenomic.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.metagenomic.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.low_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.n50_value.high_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.low_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.nr_contigs.high_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.low_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.length.high_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.path invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.coerce_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.compare_fields invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.comp_type invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.on invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param QCReportFields.checkm_contamination.high_msg invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.db invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param bakta.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param pointfinder_db_tag.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param abricate.args invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param abricate.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param abricate.header_p invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.container_version invalid: Not in pipeline parameters. Check nextflow.config.
• schema_params - Default value for param shigeifinder.report_tag invalid: Not in pipeline parameters. Check nextflow.config.
• multiqc_config - 'assets/multiqc_config.yml' does not meet requirements: Section mk-mikrokondo-summary missing in report_section_order

❗ Test warnings:

• readme - README did not have a Nextflow minimum version mentioned in Quick Start section.
• schema_lint - Schema $id should be https://raw.githubusercontent.com/mk/mikrokondo/master/nextflow_schema.json
  Found https://raw.githubusercontent.com/mk-kondo/mikrokondo/master/nextflow_schema.json
• schema_params - Schema param chopper.quality not found from nextflow config
• schema_params - Schema param chopper.minlength not found from nextflow config
• schema_params - Schema param chopper.fastq_ext not found from nextflow config
• schema_params - Schema param fastqc.html_ext not found from nextflow config
• schema_params - Schema param fastqc.zip_ext not found from nextflow config
• schema_params - Schema param mash.mash_ext not found from nextflow config
• schema_params - Schema param mash.output_reads_ext not found from nextflow config
• schema_params - Schema param mash.output_taxa_ext not found from nextflow config
• schema_params - Schema param mash.output_dir not found from nextflow config
• schema_params - Schema param mash.mash_sketch not found from nextflow config
• schema_params - Schema param mash.sketch_ext not found from nextflow config
• schema_params - Schema param mash.sketch_kmer_size not found from nextflow config
• schema_params - Schema param mash.final_sketch_name not found from nextflow config
• schema_params - Schema param r_contaminants.phix_fa not found from nextflow config
• schema_params - Schema param r_contaminants.homo_sapiens_fa not found from nextflow config
• schema_params - Schema param r_contaminants.pacbio_mg not found from nextflow config
• schema_params - Schema param r_contaminants.output_ext not found from nextflow config
• schema_params - Schema param r_contaminants.mega_mm2_idx not found from nextflow config
• schema_params - Schema param r_contaminants.mm2_illumina not found from nextflow config
• schema_params - Schema param r_contaminants.mm2_pac not found from nextflow config
• schema_params - Schema param r_contaminants.mm2_ont not found from nextflow config
• schema_params - Schema param r_contaminants.mm2_output_ext not found from nextflow config
• schema_params - Schema param r_contaminants.samtools_output_ext not found from nextflow config
• schema_params - Schema param r_contaminants.samtools_singletons_ext not found from nextflow config
• schema_params - Schema param r_contaminants.samtools_output_suffix not found from nextflow config
• schema_params - Schema param r_contaminants.output_dir not found from nextflow config
• schema_params - Schema param minimap2.index_outdir not found from nextflow config
• schema_params - Schema param minimap2.index_ext not found from nextflow config
• schema_params - Schema param minimap2.mapped_paf_ext not found from nextflow config
• schema_params - Schema param minimap2.mapped_sam_ext not found from nextflow config
• schema_params - Schema param minimap2.mapped_outdir not found from nextflow config
• schema_params - Schema param samtools.bam_ext not found from nextflow config
• schema_params - Schema param samtools.bai_ext not found from nextflow config
• schema_params - Schema param racon.consensus_suffix not found from nextflow config
• schema_params - Schema param racon.consensus_ext not found from nextflow config
• schema_params - Schema param racon.outdir not found from nextflow config
• schema_params - Schema param pilon.outdir not found from nextflow config
• schema_params - Schema param pilon.fasta_ext not found from nextflow config
• schema_params - Schema param pilon.fasta_outdir not found from nextflow config
• schema_params - Schema param pilon.vcf_ext not found from nextflow config
• schema_params - Schema param pilon.vcf_outdir not found from nextflow config
• schema_params - Schema param pilon.changes_ext not found from nextflow config
• schema_params - Schema param pilon.changes_outdir not found from nextflow config
• schema_params - Schema param pilon.max_memory_multiplier not found from nextflow config
• schema_params - Schema param pilon_iterative.outdir not found from nextflow config
• schema_params - Schema param pilon_iterative.fasta_ext not found from nextflow config
• schema_params - Schema param pilon_iterative.fasta_outdir not found from nextflow config
• schema_params - Schema param pilon_iterative.vcf_ext not found from nextflow config
• schema_params - Schema param pilon_iterative.vcf_outdir not found from nextflow config
• schema_params - Schema param pilon_iterative.bam_ext not found from nextflow config
• schema_params - Schema param pilon_iterative.bai_ext not found from nextflow config
• schema_params - Schema param pilon_iterative.changes_ext not found from nextflow config
• schema_params - Schema param pilon_iterative.changes_outdir not found from nextflow config
• schema_params - Schema param pilon_iterative.max_memory_multiplier not found from nextflow config
• schema_params - Schema param pilon_iterative.max_polishing_illumina not found from nextflow config
• schema_params - Schema param pilon_iterative.max_polishing_pacbio not found from nextflow config
• schema_params - Schema param pilon_iterative.max_polishing_nanopore not found from nextflow config
• schema_params - Schema param medaka.model not found from nextflow config
• schema_params - Schema param medaka.fasta_ext not found from nextflow config
• schema_params - Schema param medaka.outdir not found from nextflow config
• schema_params - Schema param medaka.batch_size not found from nextflow config
• schema_params - Schema param unicycler.scaffolds_ext not found from nextflow config
• schema_params - Schema param unicycler.assembly_ext not found from nextflow config
• schema_params - Schema param unicycler.log_ext not found from nextflow config
• schema_params - Schema param unicycler.outdir not found from nextflow config
• schema_params - Schema param unicycler.mem_modifier not found from nextflow config
• schema_params - Schema param unicycler.threads_increase_factor not found from nextflow config
• schema_params - Schema param bakta.output_dir not found from nextflow config
• schema_params - Schema param bakta.embl_ext not found from nextflow config
• schema_params - Schema param bakta.faa_ext not found from nextflow config
• schema_params - Schema param bakta.ffn_ext not found from nextflow config
• schema_params - Schema param bakta.fna_ext not found from nextflow config
• schema_params - Schema param bakta.gbff_ext not found from nextflow config
• schema_params - Schema param bakta.gff_ext not found from nextflow config
• schema_params - Schema param bakta.threads not found from nextflow config
• schema_params - Schema param bakta.hypotheticals_tsv_ext not found from nextflow config
• schema_params - Schema param bakta.hypotheticals_faa_ext not found from nextflow config
• schema_params - Schema param bakta.tsv_ext not found from nextflow config
• schema_params - Schema param bakta.txt_ext not found from nextflow config
• schema_params - Schema param bakta.min_contig_length not found from nextflow config
• schema_params - Schema param bandage.svg_ext not found from nextflow config
• schema_params - Schema param bandage.outdir not found from nextflow config
• schema_params - Schema param ectyper.log_ext not found from nextflow config
• schema_params - Schema param ectyper.tsv_ext not found from nextflow config
• schema_params - Schema param ectyper.txt_ext not found from nextflow config
• schema_params - Schema param ectyper.report_tag not found from nextflow config
• schema_params - Schema param sistr.tsv_ext not found from nextflow config
• schema_params - Schema param sistr.allele_fasta_ext not found from nextflow config
• schema_params - Schema param sistr.allele_json_ext not found from nextflow config
• schema_params - Schema param sistr.cgmlst_ext not found from nextflow config
• schema_params - Schema param sistr.report_tag not found from nextflow config
• schema_params - Schema param lissero.tsv_ext not found from nextflow config
• schema_params - Schema param lissero.report_tag not found from nextflow config
• schema_params - Schema param shigeifinder.tsv_ext not found from nextflow config
• schema_params - Schema param raw_reads.high_precision not found from nextflow config
• schema_params - Schema param raw_reads.report_tag not found from nextflow config
• schema_params - Schema param seqtk.assembly_fastq not found from nextflow config
• schema_params - Schema param seqtk.report_tag not found from nextflow config
• schema_params - Schema param fastp.report_exclude_fields not found from nextflow config
• schema_params - Schema param quast.header_p not found from nextflow config
• schema_params - Schema param checkm.header_p not found from nextflow config
• schema_params - Schema param kraken.header_p not found from nextflow config
• schema_params - Schema param kraken.headers not found from nextflow config
• schema_params - Schema param mlst.args not found from nextflow config
• schema_params - Schema param mlst.tsv_ext not found from nextflow config
• schema_params - Schema param mlst.json_ext not found from nextflow config
• schema_params - Schema param mlst.report_tag not found from nextflow config
• schema_params - Schema param mash.json_ext not found from nextflow config
• schema_params - Schema param mash.min_kmer not found from nextflow config
• schema_params - Schema param mash.report_tag not found from nextflow config
• schema_params - Schema param mash.header_p not found from nextflow config
• schema_params - Schema param mash.headers not found from nextflow config
• schema_params - Schema param mash_meta.report_tag not found from nextflow config
• schema_params - Schema param top_hit_species.report_tag not found from nextflow config
• schema_params - Schema param kraken_species.report_tag not found from nextflow config
• schema_params - Schema param subtyping_report.report_tag not found from nextflow config
• schema_params - Schema param ectyper.args not found from nextflow config
• schema_params - Schema param ectyper.header_p not found from nextflow config
• schema_params - Schema param kleborate.txt_ext not found from nextflow config
• schema_params - Schema param kleborate.report_tag not found from nextflow config
• schema_params - Schema param kleborate.header_p not found from nextflow config
• schema_params - Schema param spatyper.tsv_ext not found from nextflow config
• schema_params - Schema param spatyper.report_tag not found from nextflow config
• schema_params - Schema param spatyper.header_p not found from nextflow config
• schema_params - Schema param spatyper.repeats not found from nextflow config
• schema_params - Schema param spatyper.repeat_order not found from nextflow config
• schema_params - Schema param sistr.header_p not found from nextflow config
• schema_params - Schema param lissero.header_p not found from nextflow config
• schema_params - Schema param shigeifinder.header_p not found from nextflow config
• schema_params - Schema param kraken_bin.fasta_ext not found from nextflow config
• schema_params - Schema param QCReport.escherichia.search not found from nextflow config
• schema_params - Schema param QCReport.escherichia.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.escherichia.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.escherichia.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.escherichia.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.escherichia.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.escherichia.min_length not found from nextflow config
• schema_params - Schema param QCReport.escherichia.max_length not found from nextflow config
• schema_params - Schema param QCReport.escherichia.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.escherichia.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.salmonella.search not found from nextflow config
• schema_params - Schema param QCReport.salmonella.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.salmonella.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.salmonella.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.salmonella.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.salmonella.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.salmonella.min_length not found from nextflow config
• schema_params - Schema param QCReport.salmonella.max_length not found from nextflow config
• schema_params - Schema param QCReport.salmonella.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.salmonella.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.shigella.search not found from nextflow config
• schema_params - Schema param QCReport.shigella.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.shigella.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.shigella.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.shigella.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.shigella.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.shigella.min_length not found from nextflow config
• schema_params - Schema param QCReport.shigella.max_length not found from nextflow config
• schema_params - Schema param QCReport.shigella.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.shigella.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.listeria.search not found from nextflow config
• schema_params - Schema param QCReport.listeria.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.listeria.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.listeria.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.listeria.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.listeria.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.listeria.min_length not found from nextflow config
• schema_params - Schema param QCReport.listeria.max_length not found from nextflow config
• schema_params - Schema param QCReport.listeria.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.listeria.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.search not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.min_length not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.max_length not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.campylobacter.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.vibrio.search not found from nextflow config
• schema_params - Schema param QCReport.vibrio.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.vibrio.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.vibrio.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.vibrio.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.vibrio.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.vibrio.min_length not found from nextflow config
• schema_params - Schema param QCReport.vibrio.max_length not found from nextflow config
• schema_params - Schema param QCReport.vibrio.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.vibrio.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.search not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.min_length not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.max_length not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.klebsiella.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.search not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.min_length not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.max_length not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.staphylococcus.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.search not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.raw_average_quality not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.min_n50 not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.max_n50 not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.min_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.max_nr_contigs not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.min_length not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.max_length not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.max_checkm_contamination not found from nextflow config
• schema_params - Schema param QCReport.fallthrough.min_average_coverage not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.path not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.on not found from nextflow config
• schema_params - Schema param QCReportFields.raw_average_quality.low_msg not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.path not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.on not found from nextflow config
• schema_params - Schema param QCReportFields.average_coverage.low_msg not found from nextflow config
• schema_params - Schema param QCReportFields.metagenomic.path not found from nextflow config
• schema_params - Schema param QCReportFields.metagenomic.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.metagenomic.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.metagenomic.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.metagenomic.on not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.path not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.on not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.low_msg not found from nextflow config
• schema_params - Schema param QCReportFields.n50_value.high_msg not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.path not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.on not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.low_msg not found from nextflow config
• schema_params - Schema param QCReportFields.nr_contigs.high_msg not found from nextflow config
• schema_params - Schema param QCReportFields.length.path not found from nextflow config
• schema_params - Schema param QCReportFields.length.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.length.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.length.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.length.on not found from nextflow config
• schema_params - Schema param QCReportFields.length.low_msg not found from nextflow config
• schema_params - Schema param QCReportFields.length.high_msg not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.path not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.coerce_type not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.compare_fields not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.comp_type not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.on not found from nextflow config
• schema_params - Schema param QCReportFields.checkm_contamination.high_msg not found from nextflow config
• schema_params - Schema param bakta.db not found from nextflow config
• schema_params - Schema param bakta.args not found from nextflow config
• schema_params - Schema param pointfinder_db_tag.report_tag not found from nextflow config
• schema_params - Schema param abricate.args not found from nextflow config
• schema_params - Schema param abricate.report_tag not found from nextflow config
• schema_params - Schema param abricate.header_p not found from nextflow config
• schema_params - Schema param shigeifinder.container_version not found from nextflow config
• schema_params - Schema param shigeifinder.report_tag not found from nextflow config
• schema_params - Schema param coreutils.docker not found from nextflow config
• schema_params - Schema param kat.docker not found from nextflow config
• schema_params - Schema param seqtk.docker not found from nextflow config
• schema_params - Schema param fastp.docker not found from nextflow config
• schema_params - Schema param flye.docker not found from nextflow config
• schema_params - Schema param spades.docker not found from nextflow config
• schema_params - Schema param quast.docker not found from nextflow config
• schema_params - Schema param checkm.docker not found from nextflow config
• schema_params - Schema param kraken.docker not found from nextflow config
• schema_params - Schema param mlst.docker not found from nextflow config
• schema_params - Schema param mash.docker not found from nextflow config
• schema_params - Schema param r_contaminants.docker not found from nextflow config
• schema_params - Schema param minimap2.docker not found from nextflow config
• schema_params - Schema param samtools.docker not found from nextflow config
• schema_params - Schema param racon.docker not found from nextflow config
• schema_params - Schema param pilon.docker not found from nextflow config
• schema_params - Schema param pilon_iterative.docker not found from nextflow config
• schema_params - Schema param medaka.docker not found from nextflow config
• schema_params - Schema param unicycler.docker not found from nextflow config
• schema_params - Schema param bakta.docker not found from nextflow config
• schema_params - Schema param bandage.docker not found from nextflow config
• schema_params - Schema param ectyper.docker not found from nextflow config
• schema_params - Schema param kleborate.docker not found from nextflow config
• schema_params - Schema param spatyper.docker not found from nextflow config
• schema_params - Schema param sistr.docker not found from nextflow config
• schema_params - Schema param lissero.docker not found from nextflow config
• schema_params - Schema param shigeifinder.docker not found from nextflow config
• schema_params - Schema param python3.docker not found from nextflow config
• schema_params - Schema param abricate.docker not found from nextflow config
• schema_params - Schema param coreutils.singularity not found from nextflow config
• schema_params - Schema param kat.singularity not found from nextflow config
• schema_params - Schema param seqtk.singularity not found from nextflow config
• schema_params - Schema param fastp.singularity not found from nextflow config
• schema_params - Schema param chopper.singularity not found from nextflow config
• schema_params - Schema param flye.singularity not found from nextflow config
• schema_params - Schema param spades.singularity not found from nextflow config
• schema_params - Schema param quast.singularity not found from nextflow config
• schema_params - Schema param checkm.singularity not found from nextflow config
• schema_params - Schema param kraken.singularity not found from nextflow config
• schema_params - Schema param mlst.singularity not found from nextflow config
• schema_params - Schema param mash.singularity not found from nextflow config
• schema_params - Schema param r_contaminants.singularity not found from nextflow config
• schema_params - Schema param minimap2.singularity not found from nextflow config
• schema_params - Schema param samtools.singularity not found from nextflow config
• schema_params - Schema param racon.singularity not found from nextflow config
• schema_params - Schema param pilon.singularity not found from nextflow config
• schema_params - Schema param pilon_iterative.singularity not found from nextflow config
• schema_params - Schema param medaka.singularity not found from nextflow config
• schema_params - Schema param unicycler.singularity not found from nextflow config
• schema_params - Schema param bakta.singularity not found from nextflow config
• schema_params - Schema param bandage.singularity not found from nextflow config
• schema_params - Schema param ectyper.singularity not found from nextflow config
• schema_params - Schema param kleborate.singularity not found from nextflow config
• schema_params - Schema param spatyper.singularity not found from nextflow config
• schema_params - Schema param sistr.singularity not found from nextflow config
• schema_params - Schema param lissero.singularity not found from nextflow config
• schema_params - Schema param shigeifinder.singularity not found from nextflow config
• schema_params - Schema param python3.singularity not found from nextflow config
• schema_params - Schema param abricate.singularity not found from nextflow config
• schema_params - Schema param staramr.singularity not found from nextflow config
• schema_params - Schema param staramr.docker not found from nextflow config
• schema_params - Schema param staramr.db not found from nextflow config
• schema_params - Schema param staramr.tsv_ext not found from nextflow config
• schema_params - Schema param staramr.txt_ext not found from nextflow config
• schema_params - Schema param staramr.xlsx_ext not found from nextflow config
• schema_params - Schema param staramr.args not found from nextflow config
• schema_params - Schema param staramr.point_finder_dbs not found from nextflow config
• schema_params - Schema param staramr.report_tag not found from nextflow config
• schema_params - Schema param staramr.header_p not found from nextflow config
• schema_params - Schema param mobsuite_recon.singularity not found from nextflow config
• schema_params - Schema param mobsuite_recon.docker not found from nextflow config
• schema_params - Schema param mobsuite_recon.args not found from nextflow config
• schema_params - Schema param mobsuite_recon.fasta_ext not found from nextflow config
• schema_params - Schema param mobsuite_recon.results_ext not found from nextflow config
• schema_params - Schema param mobsuite_recon.mob_results_file not found from nextflow config
• schema_params - Schema param mobsuite_recon.contig_report not found from nextflow config
• schema_params - Schema param mobsuite_recon.report_tag not found from nextflow config
• schema_params - Schema param mobsuite_recon.header_p not found from nextflow config
• schema_params - Schema param kat.hist_ext not found from nextflow config
• schema_params - Schema param kat.json_ext not found from nextflow config
• schema_params - Schema param kat.png_ext not found from nextflow config
• schema_params - Schema param kat.postscript_ext not found from nextflow config
• schema_params - Schema param kat.output_type not found from nextflow config
• schema_params - Schema param kat.pdf_ext not found from nextflow config
• schema_params - Schema param kat.report_tag not found from nextflow config
• schema_params - Schema param kat.jfhash_ext not found from nextflow config
• schema_params - Schema param opt_platforms.ont not found from nextflow config
• schema_params - Schema param opt_platforms.pacbio not found from nextflow config
• schema_params - Schema param opt_platforms.hybrid not found from nextflow config
• schema_params - Schema param opt_platforms.illumina not found from nextflow config
• schema_params - Schema param seqtk.seed not found from nextflow config
• schema_params - Schema param seqtk.reads_ext not found from nextflow config
• schema_params - Schema param fastp.html_ext not found from nextflow config
• schema_params - Schema param fastp.average_quality_e not found from nextflow config
• schema_params - Schema param fastp.json_ext not found from nextflow config
• schema_params - Schema param fastp.cut_mean_quality not found from nextflow config
• schema_params - Schema param fastp.qualified_quality_phred not found from nextflow config
• schema_params - Schema param fastp.unqualified_percent_limit not found from nextflow config
• schema_params - Schema param fastp.fastq_ext not found from nextflow config
• schema_params - Schema param fastp.report_tag not found from nextflow config
• schema_params - Schema param fastp.illumina_length_min not found from nextflow config
• schema_params - Schema param fastp.single_end_length_min not found from nextflow config
• schema_params - Schema param fastp.dedup_reads not found from nextflow config
• schema_params - Schema param fastp.args.illumina not found from nextflow config
• schema_params - Schema param fastp.args.single_end not found from nextflow config
• schema_params - Schema param flye.nanopore.corr not found from nextflow config
• schema_params - Schema param flye.nanopore.hq not found from nextflow config
• schema_params - Schema param flye.pacbio.raw not found from nextflow config
• schema_params - Schema param flye.pacbio.corr not found from nextflow config
• schema_params - Schema param flye.nanopore.raw not found from nextflow config
• schema_params - Schema param flye.gfa_ext not found from nextflow config
• schema_params - Schema param flye.gv_ext not found from nextflow config
• schema_params - Schema param flye.txt_ext not found from nextflow config
• schema_params - Schema param flye.log_ext not found from nextflow config
• schema_params - Schema param flye.json_ext not found from nextflow config
• schema_params - Schema param flye.polishing_iterations not found from nextflow config
• schema_params - Schema param flye.fasta_ext not found from nextflow config
• schema_params - Schema param flye.pacbio.hq not found from nextflow config
• schema_params - Schema param flye.args not found from nextflow config
• schema_params - Schema param quast.suffix not found from nextflow config
• schema_params - Schema param quast.report_base not found from nextflow config
• schema_params - Schema param quast.report_prefix not found from nextflow config
• schema_params - Schema param quast.report_ext not found from nextflow config
• schema_params - Schema param quast.report_tag not found from nextflow config
• schema_params - Schema param quast_filter.n50_field not found from nextflow config
• schema_params - Schema param quast_filter.n50_value not found from nextflow config
• schema_params - Schema param quast_filter.nr_contigs_field not found from nextflow config
• schema_params - Schema param quast_filter.nr_contigs_value not found from nextflow config
• schema_params - Schema param quast_filter.sample_header not found from nextflow config
• schema_params - Schema param quast.min_contig_length not found from nextflow config
• schema_params - Schema param quast.args not found from nextflow config
• schema_params - Schema param spades.scaffolds_ext not found from nextflow config
• schema_params - Schema param spades.contigs_ext not found from nextflow config
• schema_params - Schema param spades.transcripts_ext not found from nextflow config
• schema_params - Schema param spades.gene_clusters_ext not found from nextflow config
• schema_params - Schema param spades.assembly_graphs_ext not found from nextflow config
• schema_params - Schema param spades.log_ext not found from nextflow config
• schema_params - Schema param spades.outdir not found from nextflow config
• schema_params - Schema param checkm.alignment_ext not found from nextflow config
• schema_params - Schema param checkm.results_ext not found from nextflow config
• schema_params - Schema param checkm.tsv_ext not found from nextflow config
• schema_params - Schema param checkm.folder_name not found from nextflow config
• schema_params - Schema param checkm.gzip_ext not found from nextflow config
• schema_params - Schema param checkm.lineage_ms not found from nextflow config
• schema_params - Schema param checkm.report_tag not found from nextflow config
• schema_params - Schema param kraken.db not found from nextflow config
• schema_params - Schema param kraken.classified_suffix not found from nextflow config
• schema_params - Schema param kraken.unclassified_suffix not found from nextflow config
• schema_params - Schema param kraken.report_suffix not found from nextflow config
• schema_params - Schema param kraken.output_suffix not found from nextflow config
• schema_params - Schema param kraken.save_output_fastqs not found from nextflow config
• schema_params - Schema param kraken.save_reads_assignments not found from nextflow config
• schema_params - Schema param kraken.run_kraken_quick not found from nextflow config
• schema_params - Schema param kraken.report_tag not found from nextflow config
• schema_params - Schema param kraken.tophit_level not found from nextflow config
• schema_params - Schema param kraken_bin.taxonomic_level not found from nextflow config
• schema_description - Ungrouped param in schema: chopper.quality
• schema_description - Ungrouped param in schema: chopper.minlength
• schema_description - Ungrouped param in schema: chopper.fastq_ext
• schema_description - Ungrouped param in schema: fastqc.html_ext
• schema_description - Ungrouped param in schema: fastqc.zip_ext
• schema_description - Ungrouped param in schema: mash.mash_ext
• schema_description - Ungrouped param in schema: mash.output_reads_ext
• schema_description - Ungrouped param in schema: mash.output_taxa_ext
• schema_description - Ungrouped param in schema: mash.output_dir
• schema_description - Ungrouped param in schema: mash.mash_sketch
• schema_description - Ungrouped param in schema: mash.sketch_ext
• schema_description - Ungrouped param in schema: mash.sketch_kmer_size
• schema_description - Ungrouped param in schema: mash.final_sketch_name
• schema_description - Ungrouped param in schema: r_contaminants.phix_fa
• schema_description - Ungrouped param in schema: r_contaminants.homo_sapiens_fa
• schema_description - Ungrouped param in schema: r_contaminants.pacbio_mg
• schema_description - Ungrouped param in schema: r_contaminants.output_ext
• schema_description - Ungrouped param in schema: r_contaminants.mega_mm2_idx
• schema_description - Ungrouped param in schema: r_contaminants.mm2_illumina
• schema_description - Ungrouped param in schema: r_contaminants.mm2_pac
• schema_description - Ungrouped param in schema: r_contaminants.mm2_ont
• schema_description - Ungrouped param in schema: r_contaminants.mm2_output_ext
• schema_description - Ungrouped param in schema: r_contaminants.samtools_output_ext
• schema_description - Ungrouped param in schema: r_contaminants.samtools_singletons_ext
• schema_description - Ungrouped param in schema: r_contaminants.samtools_output_suffix
• schema_description - Ungrouped param in schema: r_contaminants.output_dir
• schema_description - Ungrouped param in schema: minimap2.index_outdir
• schema_description - Ungrouped param in schema: minimap2.index_ext
• schema_description - Ungrouped param in schema: minimap2.mapped_paf_ext
• schema_description - Ungrouped param in schema: minimap2.mapped_sam_ext
• schema_description - Ungrouped param in schema: minimap2.mapped_outdir
• schema_description - Ungrouped param in schema: samtools.bam_ext
• schema_description - Ungrouped param in schema: samtools.bai_ext
• schema_description - Ungrouped param in schema: racon.consensus_suffix
• schema_description - Ungrouped param in schema: racon.consensus_ext
• schema_description - Ungrouped param in schema: racon.outdir
• schema_description - Ungrouped param in schema: pilon.outdir
• schema_description - Ungrouped param in schema: pilon.fasta_ext
• schema_description - Ungrouped param in schema: pilon.fasta_outdir
• schema_description - Ungrouped param in schema: pilon.vcf_ext
• schema_description - Ungrouped param in schema: pilon.vcf_outdir
• schema_description - Ungrouped param in schema: pilon.changes_ext
• schema_description - Ungrouped param in schema: pilon.changes_outdir
• schema_description - Ungrouped param in schema: pilon.max_memory_multiplier
• schema_description - Ungrouped param in schema: pilon_iterative.outdir
• schema_description - Ungrouped param in schema: pilon_iterative.fasta_ext
• schema_description - Ungrouped param in schema: pilon_iterative.fasta_outdir
• schema_description - Ungrouped param in schema: pilon_iterative.vcf_ext
• schema_description - Ungrouped param in schema: pilon_iterative.vcf_outdir
• schema_description - Ungrouped param in schema: pilon_iterative.bam_ext
• schema_description - Ungrouped param in schema: pilon_iterative.bai_ext
• schema_description - Ungrouped param in schema: pilon_iterative.changes_ext
• schema_description - Ungrouped param in schema: pilon_iterative.changes_outdir
• schema_description - Ungrouped param in schema: pilon_iterative.max_memory_multiplier
• schema_description - Ungrouped param in schema: pilon_iterative.max_polishing_illumina
• schema_description - Ungrouped param in schema: pilon_iterative.max_polishing_pacbio
• schema_description - Ungrouped param in schema: pilon_iterative.max_polishing_nanopore
• schema_description - Ungrouped param in schema: medaka.model
• schema_description - Ungrouped param in schema: medaka.fasta_ext
• schema_description - Ungrouped param in schema: medaka.outdir
• schema_description - Ungrouped param in schema: medaka.batch_size
• schema_description - Ungrouped param in schema: unicycler.scaffolds_ext
• schema_description - Ungrouped param in schema: unicycler.assembly_ext
• schema_description - Ungrouped param in schema: unicycler.log_ext
• schema_description - Ungrouped param in schema: unicycler.outdir
• schema_description - Ungrouped param in schema: unicycler.mem_modifier
• schema_description - Ungrouped param in schema: unicycler.threads_increase_factor
• schema_description - Ungrouped param in schema: bakta.output_dir
• schema_description - Ungrouped param in schema: bakta.embl_ext
• schema_description - Ungrouped param in schema: bakta.faa_ext
• schema_description - Ungrouped param in schema: bakta.ffn_ext
• schema_description - Ungrouped param in schema: bakta.fna_ext
• schema_description - Ungrouped param in schema: bakta.gbff_ext
• schema_description - Ungrouped param in schema: bakta.gff_ext
• schema_description - Ungrouped param in schema: bakta.threads
• schema_description - Ungrouped param in schema: bakta.hypotheticals_tsv_ext
• schema_description - Ungrouped param in schema: bakta.hypotheticals_faa_ext
• schema_description - Ungrouped param in schema: bakta.tsv_ext
• schema_description - Ungrouped param in schema: bakta.txt_ext
• schema_description - Ungrouped param in schema: bakta.min_contig_length
• schema_description - Ungrouped param in schema: bandage.svg_ext
• schema_description - Ungrouped param in schema: bandage.outdir
• schema_description - Ungrouped param in schema: ectyper.log_ext
• schema_description - Ungrouped param in schema: ectyper.tsv_ext
• schema_description - Ungrouped param in schema: ectyper.txt_ext
• schema_description - Ungrouped param in schema: ectyper.report_tag
• schema_description - Ungrouped param in schema: sistr.tsv_ext
• schema_description - Ungrouped param in schema: sistr.allele_fasta_ext
• schema_description - Ungrouped param in schema: sistr.allele_json_ext
• schema_description - Ungrouped param in schema: sistr.cgmlst_ext
• schema_description - Ungrouped param in schema: sistr.report_tag
• schema_description - Ungrouped param in schema: lissero.tsv_ext
• schema_description - Ungrouped param in schema: lissero.report_tag
• schema_description - Ungrouped param in schema: shigeifinder.tsv_ext
• schema_description - Ungrouped param in schema: target_depth
• schema_description - Ungrouped param in schema: raw_reads.high_precision
• schema_description - Ungrouped param in schema: raw_reads.report_tag
• schema_description - Ungrouped param in schema: seqtk.assembly_fastq
• schema_description - Ungrouped param in schema: seqtk.report_tag
• schema_description - Ungrouped param in schema: fastp.report_exclude_fields
• schema_description - Ungrouped param in schema: quast.header_p
• schema_description - Ungrouped param in schema: checkm.header_p
• schema_description - Ungrouped param in schema: kraken.header_p
• schema_description - Ungrouped param in schema: kraken.headers
• schema_description - Ungrouped param in schema: mlst.args
• schema_description - Ungrouped param in schema: mlst.tsv_ext
• schema_description - Ungrouped param in schema: mlst.json_ext
• schema_description - Ungrouped param in schema: mlst.report_tag
• schema_description - Ungrouped param in schema: mash.json_ext
• schema_description - Ungrouped param in schema: mash.min_kmer
• schema_description - Ungrouped param in schema: mash.report_tag
• schema_description - Ungrouped param in schema: mash.header_p
• schema_description - Ungrouped param in schema: mash.headers
• schema_description - Ungrouped param in schema: mash_meta.report_tag
• schema_description - Ungrouped param in schema: top_hit_species.report_tag
• schema_description - Ungrouped param in schema: kraken_species.report_tag
• schema_description - Ungrouped param in schema: subtyping_report.report_tag
• schema_description - Ungrouped param in schema: ectyper.args
• schema_description - Ungrouped param in schema: ectyper.header_p
• schema_description - Ungrouped param in schema: kleborate.txt_ext
• schema_description - Ungrouped param in schema: kleborate.report_tag
• schema_description - Ungrouped param in schema: kleborate.header_p
• schema_description - Ungrouped param in schema: spatyper.tsv_ext
• schema_description - Ungrouped param in schema: spatyper.report_tag
• schema_description - Ungrouped param in schema: spatyper.header_p
• schema_description - Ungrouped param in schema: spatyper.repeats
• schema_description - Ungrouped param in schema: spatyper.repeat_order
• schema_description - Ungrouped param in schema: sistr.header_p
• schema_description - Ungrouped param in schema: lissero.header_p
• schema_description - Ungrouped param in schema: shigeifinder.header_p
• schema_description - Ungrouped param in schema: kraken_bin.fasta_ext
• schema_description - Ungrouped param in schema: QCReport.escherichia.search
• schema_description - Ungrouped param in schema: QCReport.escherichia.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.escherichia.min_n50
• schema_description - Ungrouped param in schema: QCReport.escherichia.max_n50
• schema_description - Ungrouped param in schema: QCReport.escherichia.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.escherichia.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.escherichia.min_length
• schema_description - Ungrouped param in schema: QCReport.escherichia.max_length
• schema_description - Ungrouped param in schema: QCReport.escherichia.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.escherichia.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.salmonella.search
• schema_description - Ungrouped param in schema: QCReport.salmonella.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.salmonella.min_n50
• schema_description - Ungrouped param in schema: QCReport.salmonella.max_n50
• schema_description - Ungrouped param in schema: QCReport.salmonella.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.salmonella.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.salmonella.min_length
• schema_description - Ungrouped param in schema: QCReport.salmonella.max_length
• schema_description - Ungrouped param in schema: QCReport.salmonella.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.salmonella.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.shigella.search
• schema_description - Ungrouped param in schema: QCReport.shigella.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.shigella.min_n50
• schema_description - Ungrouped param in schema: QCReport.shigella.max_n50
• schema_description - Ungrouped param in schema: QCReport.shigella.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.shigella.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.shigella.min_length
• schema_description - Ungrouped param in schema: QCReport.shigella.max_length
• schema_description - Ungrouped param in schema: QCReport.shigella.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.shigella.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.listeria.search
• schema_description - Ungrouped param in schema: QCReport.listeria.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.listeria.min_n50
• schema_description - Ungrouped param in schema: QCReport.listeria.max_n50
• schema_description - Ungrouped param in schema: QCReport.listeria.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.listeria.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.listeria.min_length
• schema_description - Ungrouped param in schema: QCReport.listeria.max_length
• schema_description - Ungrouped param in schema: QCReport.listeria.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.listeria.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.campylobacter.search
• schema_description - Ungrouped param in schema: QCReport.campylobacter.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.campylobacter.min_n50
• schema_description - Ungrouped param in schema: QCReport.campylobacter.max_n50
• schema_description - Ungrouped param in schema: QCReport.campylobacter.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.campylobacter.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.campylobacter.min_length
• schema_description - Ungrouped param in schema: QCReport.campylobacter.max_length
• schema_description - Ungrouped param in schema: QCReport.campylobacter.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.campylobacter.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.vibrio.search
• schema_description - Ungrouped param in schema: QCReport.vibrio.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.vibrio.min_n50
• schema_description - Ungrouped param in schema: QCReport.vibrio.max_n50
• schema_description - Ungrouped param in schema: QCReport.vibrio.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.vibrio.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.vibrio.min_length
• schema_description - Ungrouped param in schema: QCReport.vibrio.max_length
• schema_description - Ungrouped param in schema: QCReport.vibrio.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.vibrio.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.klebsiella.search
• schema_description - Ungrouped param in schema: QCReport.klebsiella.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.klebsiella.min_n50
• schema_description - Ungrouped param in schema: QCReport.klebsiella.max_n50
• schema_description - Ungrouped param in schema: QCReport.klebsiella.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.klebsiella.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.klebsiella.min_length
• schema_description - Ungrouped param in schema: QCReport.klebsiella.max_length
• schema_description - Ungrouped param in schema: QCReport.klebsiella.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.klebsiella.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.search
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.min_n50
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.max_n50
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.min_length
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.max_length
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.staphylococcus.min_average_coverage
• schema_description - Ungrouped param in schema: QCReport.fallthrough.search
• schema_description - Ungrouped param in schema: QCReport.fallthrough.raw_average_quality
• schema_description - Ungrouped param in schema: QCReport.fallthrough.min_n50
• schema_description - Ungrouped param in schema: QCReport.fallthrough.max_n50
• schema_description - Ungrouped param in schema: QCReport.fallthrough.min_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.fallthrough.max_nr_contigs
• schema_description - Ungrouped param in schema: QCReport.fallthrough.min_length
• schema_description - Ungrouped param in schema: QCReport.fallthrough.max_length
• schema_description - Ungrouped param in schema: QCReport.fallthrough.max_checkm_contamination
• schema_description - Ungrouped param in schema: QCReport.fallthrough.min_average_coverage
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.path
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.on
• schema_description - Ungrouped param in schema: QCReportFields.raw_average_quality.low_msg
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.path
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.on
• schema_description - Ungrouped param in schema: QCReportFields.average_coverage.low_msg
• schema_description - Ungrouped param in schema: QCReportFields.metagenomic.path
• schema_description - Ungrouped param in schema: QCReportFields.metagenomic.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.metagenomic.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.metagenomic.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.metagenomic.on
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.path
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.on
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.low_msg
• schema_description - Ungrouped param in schema: QCReportFields.n50_value.high_msg
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.path
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.on
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.low_msg
• schema_description - Ungrouped param in schema: QCReportFields.nr_contigs.high_msg
• schema_description - Ungrouped param in schema: QCReportFields.length.path
• schema_description - Ungrouped param in schema: QCReportFields.length.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.length.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.length.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.length.on
• schema_description - Ungrouped param in schema: QCReportFields.length.low_msg
• schema_description - Ungrouped param in schema: QCReportFields.length.high_msg
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.path
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.coerce_type
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.compare_fields
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.comp_type
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.on
• schema_description - Ungrouped param in schema: QCReportFields.checkm_contamination.high_msg
• schema_description - Ungrouped param in schema: bakta.db
• schema_description - Ungrouped param in schema: bakta.args
• schema_description - Ungrouped param in schema: flye_read_type
• schema_description - Ungrouped param in schema: pointfinder_db_tag.report_tag
• schema_description - Ungrouped param in schema: abricate.args
• schema_description - Ungrouped param in schema: abricate.report_tag
• schema_description - Ungrouped param in schema: abricate.header_p
• schema_description - Ungrouped param in schema: shigeifinder.container_version
• schema_description - Ungrouped param in schema: shigeifinder.report_tag
• schema_description - Ungrouped param in schema: validationS3PathCheck
• schema_description - No description provided in schema for parameter: coreutils.docker
• schema_description - No description provided in schema for parameter: kat.docker
• schema_description - No description provided in schema for parameter: seqtk.docker
• schema_description - No description provided in schema for parameter: fastp.docker
• schema_description - No description provided in schema for parameter: flye.docker
• schema_description - No description provided in schema for parameter: spades.docker
• schema_description - No description provided in schema for parameter: quast.docker
• schema_description - No description provided in schema for parameter: checkm.docker
• schema_description - No description provided in schema for parameter: kraken.docker
• schema_description - No description provided in schema for parameter: mlst.docker
• schema_description - No description provided in schema for parameter: mash.docker
• schema_description - No description provided in schema for parameter: r_contaminants.docker
• schema_description - No description provided in schema for parameter: minimap2.docker
• schema_description - No description provided in schema for parameter: samtools.docker
• schema_description - No description provided in schema for parameter: racon.docker
• schema_description - No description provided in schema for parameter: pilon.docker
• schema_description - No description provided in schema for parameter: pilon_iterative.docker
• schema_description - No description provided in schema for parameter: medaka.docker
• schema_description - No description provided in schema for parameter: unicycler.docker
• schema_description - No description provided in schema for parameter: bakta.docker
• schema_description - No description provided in schema for parameter: bandage.docker
• schema_description - No description provided in schema for parameter: ectyper.docker
• schema_description - No description provided in schema for parameter: kleborate.docker
• schema_description - No description provided in schema for parameter: spatyper.docker
• schema_description - No description provided in schema for parameter: sistr.docker
• schema_description - No description provided in schema for parameter: lissero.docker
• schema_description - No description provided in schema for parameter: shigeifinder.docker
• schema_description - No description provided in schema for parameter: python3.docker
• schema_description - No description provided in schema for parameter: abricate.docker
• schema_description - No description provided in schema for parameter: coreutils.singularity
• schema_description - No description provided in schema for parameter: kat.singularity
• schema_description - No description provided in schema for parameter: seqtk.singularity
• schema_description - No description provided in schema for parameter: fastp.singularity
• schema_description - No description provided in schema for parameter: chopper.singularity
• schema_description - No description provided in schema for parameter: flye.singularity
• schema_description - No description provided in schema for parameter: spades.singularity
• schema_description - No description provided in schema for parameter: quast.singularity
• schema_description - No description provided in schema for parameter: checkm.singularity
• schema_description - No description provided in schema for parameter: kraken.singularity
• schema_description - No description provided in schema for parameter: mlst.singularity
• schema_description - No description provided in schema for parameter: mash.singularity
• schema_description - No description provided in schema for parameter: r_contaminants.singularity
• schema_description - No description provided in schema for parameter: minimap2.singularity
• schema_description - No description provided in schema for parameter: samtools.singularity
• schema_description - No description provided in schema for parameter: racon.singularity
• schema_description - No description provided in schema for parameter: pilon.singularity
• schema_description - No description provided in schema for parameter: pilon_iterative.singularity
• schema_description - No description provided in schema for parameter: medaka.singularity
• schema_description - No description provided in schema for parameter: unicycler.singularity
• schema_description - No description provided in schema for parameter: bakta.singularity
• schema_description - No description provided in schema for parameter: bandage.singularity
• schema_description - No description provided in schema for parameter: ectyper.singularity
• schema_description - No description provided in schema for parameter: kleborate.singularity
• schema_description - No description provided in schema for parameter: spatyper.singularity
• schema_description - No description provided in schema for parameter: sistr.singularity
• schema_description - No description provided in schema for parameter: lissero.singularity
• schema_description - No description provided in schema for parameter: shigeifinder.singularity
• schema_description - No description provided in schema for parameter: python3.singularity
• schema_description - No description provided in schema for parameter: abricate.singularity
• schema_description - No description provided in schema for parameter: staramr.singularity
• schema_description - No description provided in schema for parameter: staramr.docker
• schema_description - No description provided in schema for parameter: staramr.db
• schema_description - No description provided in schema for parameter: staramr.tsv_ext
• schema_description - No description provided in schema for parameter: staramr.txt_ext
• schema_description - No description provided in schema for parameter: staramr.xlsx_ext
• schema_description - No description provided in schema for parameter: staramr.args
• schema_description - No description provided in schema for parameter: staramr.point_finder_dbs
• schema_description - No description provided in schema for parameter: staramr.report_tag
• schema_description - No description provided in schema for parameter: staramr.header_p
• schema_description - No description provided in schema for parameter: skip_depth_sampling
• schema_description - No description provided in schema for parameter: skip_subtyping
• schema_description - No description provided in schema for parameter: skip_polishing
• schema_description - No description provided in schema for parameter: skip_ont_header_cleaning
• schema_description - No description provided in schema for parameter: skip_checkm
• schema_description - No description provided in schema for parameter: skip_report
• schema_description - No description provided in schema for parameter: skip_raw_read_metrics
• schema_description - No description provided in schema for parameter: skip_version_gathering
• schema_description - No description provided in schema for parameter: skip_abricate
• schema_description - No description provided in schema for parameter: skip_bakta
• schema_description - No description provided in schema for parameter: skip_species_classification
• schema_description - No description provided in schema for parameter: skip_mlst
• schema_description - No description provided in schema for parameter: skip_mobrecon
• schema_description - No description provided in schema for parameter: skip_staramr
• schema_description - No description provided in schema for parameter: mobsuite_recon.singularity
• schema_description - No description provided in schema for parameter: mobsuite_recon.docker
• schema_description - No description provided in schema for parameter: mobsuite_recon.args
• schema_description - No description provided in schema for parameter: mobsuite_recon.fasta_ext
• schema_description - No description provided in schema for parameter: mobsuite_recon.results_ext
• schema_description - No description provided in schema for parameter: mobsuite_recon.mob_results_file
• schema_description - No description provided in schema for parameter: mobsuite_recon.contig_report
• schema_description - No description provided in schema for parameter: mobsuite_recon.report_tag
• schema_description - No description provided in schema for parameter: mobsuite_recon.header_p
• schema_description - No description provided in schema for parameter: output_idx_name
• schema_description - No description provided in schema for parameter: platform
• schema_description - No description provided in schema for parameter: nanopore_chemistry
• schema_description - No description provided in schema for parameter: run_kraken
• schema_description - No description provided in schema for parameter: hybrid_unicycler
• schema_description - No description provided in schema for parameter: long_read_opt
• schema_description - No description provided in schema for parameter: min_reads
• schema_description - No description provided in schema for parameter: metagenomic_run
• schema_description - No description provided in schema for parameter: stage_in_mode
• schema_description - No description provided in schema for parameter: slurm_p
• schema_description - No description provided in schema for parameter: slurm_profile
• schema_description - No description provided in schema for parameter: schema_ignore_params
• schema_description - No description provided in schema for parameter: kat.hist_ext
• schema_description - No description provided in schema for parameter: kat.json_ext
• schema_description - No description provided in schema for parameter: kat.png_ext
• schema_description - No description provided in schema for parameter: kat.postscript_ext
• schema_description - No description provided in schema for parameter: kat.output_type
• schema_description - No description provided in schema for parameter: kat.pdf_ext
• schema_description - No description provided in schema for parameter: kat.report_tag
• schema_description - No description provided in schema for parameter: kat.jfhash_ext
• schema_description - No description provided in schema for parameter: opt_platforms.ont
• schema_description - No description provided in schema for parameter: opt_platforms.pacbio
• schema_description - No description provided in schema for parameter: opt_platforms.hybrid
• schema_description - No description provided in schema for parameter: opt_platforms.illumina
• schema_description - No description provided in schema for parameter: seqtk.seed
• schema_description - No description provided in schema for parameter: seqtk.reads_ext
• schema_description - No description provided in schema for parameter: fastp.html_ext
• schema_description - No description provided in schema for parameter: fastp.average_quality_e
• schema_description - No description provided in schema for parameter: fastp.json_ext
• schema_description - No description provided in schema for parameter: fastp.cut_mean_quality
• schema_description - No description provided in schema for parameter: fastp.qualified_quality_phred
• schema_description - No description provided in schema for parameter: fastp.unqualified_percent_limit
• schema_description - No description provided in schema for parameter: fastp.fastq_ext
• schema_description - No description provided in schema for parameter: fastp.report_tag
• schema_description - No description provided in schema for parameter: fastp.illumina_length_min
• schema_description - No description provided in schema for parameter: fastp.single_end_length_min
• schema_description - No description provided in schema for parameter: fastp.dedup_reads
• schema_description - No description provided in schema for parameter: fastp.args.illumina
• schema_description - No description provided in schema for parameter: fastp.args.single_end
• schema_description - No description provided in schema for parameter: flye.nanopore.corr
• schema_description - No description provided in schema for parameter: flye.nanopore.hq
• schema_description - No description provided in schema for parameter: flye.pacbio.raw
• schema_description - No description provided in schema for parameter: flye.pacbio.corr
• schema_description - No description provided in schema for parameter: flye.nanopore.raw
• schema_description - No description provided in schema for parameter: flye.gfa_ext
• schema_description - No description provided in schema for parameter: flye.gv_ext
• schema_description - No description provided in schema for parameter: flye.txt_ext
• schema_description - No description provided in schema for parameter: flye.log_ext
• schema_description - No description provided in schema for parameter: flye.json_ext
• schema_description - No description provided in schema for parameter: flye.polishing_iterations
• schema_description - No description provided in schema for parameter: flye.fasta_ext
• schema_description - No description provided in schema for parameter: flye.pacbio.hq
• schema_description - No description provided in schema for parameter: flye.args
• schema_description - No description provided in schema for parameter: quast.suffix
• schema_description - No description provided in schema for parameter: quast.report_base
• schema_description - No description provided in schema for parameter: quast.report_prefix
• schema_description - No description provided in schema for parameter: quast.report_ext
• schema_description - No description provided in schema for parameter: quast.report_tag
• schema_description - No description provided in schema for parameter: quast_filter.n50_field
• schema_description - No description provided in schema for parameter: quast_filter.n50_value
• schema_description - No description provided in schema for parameter: quast_filter.nr_contigs_field
• schema_description - No description provided in schema for parameter: quast_filter.nr_contigs_value
• schema_description - No description provided in schema for parameter: quast_filter.sample_header
• schema_description - No description provided in schema for parameter: quast.min_contig_length
• schema_description - No description provided in schema for parameter: quast.args
• schema_description - No description provided in schema for parameter: spades.scaffolds_ext
• schema_description - No description provided in schema for parameter: spades.contigs_ext
• schema_description - No description provided in schema for parameter: spades.transcripts_ext
• schema_description - No description provided in schema for parameter: spades.gene_clusters_ext
• schema_description - No description provided in schema for parameter: spades.assembly_graphs_ext
• schema_description - No description provided in schema for parameter: spades.log_ext
• schema_description - No description provided in schema for parameter: spades.outdir
• schema_description - No description provided in schema for parameter: checkm.alignment_ext
• schema_description - No description provided in schema for parameter: checkm.results_ext
• schema_description - No description provided in schema for parameter: checkm.tsv_ext
• schema_description - No description provided in schema for parameter: checkm.folder_name
• schema_description - No description provided in schema for parameter: checkm.gzip_ext
• schema_description - No description provided in schema for parameter: checkm.lineage_ms
• schema_description - No description provided in schema for parameter: checkm.report_tag
• schema_description - No description provided in schema for parameter: kraken.db
• schema_description - No description provided in schema for parameter: kraken.classified_suffix
• schema_description - No description provided in schema for parameter: kraken.unclassified_suffix
• schema_description - No description provided in schema for parameter: kraken.report_suffix
• schema_description - No description provided in schema for parameter: kraken.output_suffix
• schema_description - No description provided in schema for parameter: kraken.save_output_fastqs
• schema_description - No description provided in schema for parameter: kraken.save_reads_assignments
• schema_description - No description provided in schema for parameter: kraken.run_kraken_quick
• schema_description - No description provided in schema for parameter: kraken.report_tag
• schema_description - No description provided in schema for parameter: kraken.tophit_level

❔ Tests ignored:

• files_exist - File is ignored: CODE_OF_CONDUCT.md
• files_exist - File is ignored: assets/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_light.png
• files_exist - File is ignored: docs/images/nf-core-mikrokondo_logo_dark.png
• files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
• files_exist - File is ignored: .github/workflows/awstest.yml
• files_exist - File is ignored: .github/workflows/awsfulltest.yml
• nextflow_config - Config variable ignored: manifest.name
• nextflow_config - Config variable ignored: manifest.homePage
• files_unchanged - File does not exist: .gitattributes
• files_unchanged - File does not exist: CODE_OF_CONDUCT.md
• files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
• files_unchanged - File does not exist: .github/workflows/branch.yml
• files_unchanged - File does not exist: assets/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_light.png
• files_unchanged - File does not exist: docs/images/nf-core-mikrokondo_logo_dark.png
• files_unchanged - File does not exist: docs/README.md
• actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml

✅ Tests passed:

• files_exist - File found: .gitignore
• files_exist - File found: .nf-core.yml
• files_exist - File found: .prettierignore
• files_exist - File found: .prettierrc.yml
• files_exist - File found: CHANGELOG.md
• files_exist - File found: CITATIONS.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.yml
• files_exist - File found: .github/ISSUE_TEMPLATE/feature_request.yml
• files_exist - File found: .github/PULL_REQUEST_TEMPLATE.md
• 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: conf/modules.config
• files_exist - File found: conf/test.config
• files_exist - File found: conf/test_full.config
• files_exist - File found: lib/nfcore_external_java_deps.jar
• files_exist - File found: lib/NfcoreSchema.groovy
• files_exist - File found: lib/NfcoreTemplate.groovy
• files_exist - File found: lib/Utils.groovy
• files_exist - File found: lib/WorkflowMain.groovy
• files_exist - File found: main.nf
• files_exist - File found: assets/multiqc_config.yml
• files_exist - File found: conf/base.config
• files_exist - File found: conf/igenomes.config
• files_exist - File found: lib/WorkflowMikrokondo.groovy
• files_exist - File found: modules.json
• files_exist - File found: pyproject.toml
• files_exist - File not found check: Singularity
• files_exist - File not found check: parameters.settings.json
• files_exist - File not found check: .nf-core.yaml
• 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: .github/ISSUE_TEMPLATE/bug_report.md
• files_exist - File not found check: .github/ISSUE_TEMPLATE/feature_request.md
• files_exist - File not found check: docs/images/nf-core-mikrokondo_logo.png
• files_exist - File not found check: .markdownlint.yml
• files_exist - File not found check: .yamllint.yml
• files_exist - File not found check: lib/Checks.groovy
• files_exist - File not found check: lib/Completion.groovy
• files_exist - File not found check: lib/Workflow.groovy
• files_exist - File not found check: .travis.yml
• 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: 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 (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 variable (correctly) not found: params.enable_conda
• 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 dag.file ended with .html
• nextflow_config - Config variable manifest.nextflowVersion started with >= or !>=
• nextflow_config - Config manifest.version ends in dev: '1.0dev'
• 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
• files_unchanged - .prettierrc.yml matches the template
• files_unchanged - .github/.dockstore.yml matches the template
• files_unchanged - .github/workflows/linting.yml matches the template
• files_unchanged - lib/nfcore_external_java_deps.jar matches the template
• files_unchanged - lib/NfcoreTemplate.groovy matches the template
• files_unchanged - .prettierignore matches the template
• files_unchanged - pyproject.toml matches the template
• readme - README Nextflow minimum version badge matched config. Badge: 22.10.1, Config: 22.10.1
• pipeline_todos - No TODO strings found
• pipeline_name_conventions - Name adheres to nf-core convention
• template_strings - Did not find any Jinja template strings (162 files)
• schema_lint - Schema lint passed
• schema_lint - Input mimetype lint passed: 'text/csv'
• actions_schema_validation - Workflow validation passed: fix-linting.yml
• actions_schema_validation - Workflow validation passed: stub.yml
• actions_schema_validation - Workflow validation passed: linting_comment.yml
• actions_schema_validation - Workflow validation passed: linting.yml
• actions_schema_validation - Workflow validation passed: ci.yml
• merge_markers - No merge markers found in pipeline files
• modules_json - Only installed modules found in modules.json
• multiqc_config - 'assets/multiqc_config.yml' contains 'export_plots: true'.
• modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

• nf-core/tools version 2.7.2
• Run at 2023-10-31 18:46:37