Add/linting #37

apetkau · 2024-03-07T21:55:32Z

Adds GitHub action to run nf-core lint
Fixes some of the linting issues
Configures other issues to be ignored. They will still be included in a PR comment so they are visible and we can slowly start addressing them.
Removed unneeded defaults in nextflow_schema.json

github-actions · 2024-03-08T16:02:56Z

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

Posted for pipeline commit aee9847

+| ✅  75 tests passed       |+
#| ❔  31 tests were ignored |#
!| ❗ 459 tests had warnings |!

❗ Test warnings:

readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
schema_lint - Schema title should be phac-nml/mikrokondo pipeline parameters
Found: mikrokondo pipeline parameters
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: 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: 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: bakta.db
schema_description - Ungrouped param in schema: bakta.args
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: validationFailUnrecognisedParams
schema_description - Ungrouped param in schema: fastp.cut_tail_mean_quality
schema_description - Ungrouped param in schema: fastp.complexity_threshold
schema_description - Ungrouped param in schema: fastp.polyg_min_len
schema_description - Ungrouped param in schema: fastp.polyx_min_len
schema_description - Ungrouped param in schema: fastp.illumina_length_max
schema_description - Ungrouped param in schema: assembly_status.report_tag
schema_description - Ungrouped param in schema: filtered_reads.threshold
schema_description - Ungrouped param in schema: filtered_reads.report_tag
schema_description - Ungrouped param in schema: fastp.cut_tail_window_size
schema_description - Ungrouped param in schema: contigs_too_short.report_tag
schema_description - No description provided in schema for parameter: seqkit.singularity
schema_description - No description provided in schema for parameter: seqkit.docker
schema_description - No description provided in schema for parameter: seqkit.report_ext
schema_description - No description provided in schema for parameter: seqkit.fasta_ext
schema_description - No description provided in schema for parameter: seqkit.filter_field
schema_description - No description provided in schema for parameter: seqkit.report_tag
schema_description - No description provided in schema for parameter: seqkit.header_p
schema_description - No description provided in schema for parameter: coverage_calc_fields.fixed_cov
schema_description - No description provided in schema for parameter: coverage_calc_fields.auto_cov
schema_description - No description provided in schema for parameter: coverage_calc_fields.bp_field
schema_description - No description provided in schema for parameter: QCReport.escherichia.search
schema_description - No description provided in schema for parameter: QCReport.escherichia.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.escherichia.min_n50
schema_description - No description provided in schema for parameter: QCReport.escherichia.max_n50
schema_description - No description provided in schema for parameter: QCReport.escherichia.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.escherichia.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.escherichia.min_length
schema_description - No description provided in schema for parameter: QCReport.escherichia.max_length
schema_description - No description provided in schema for parameter: QCReport.escherichia.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.escherichia.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.salmonella.search
schema_description - No description provided in schema for parameter: QCReport.salmonella.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.salmonella.min_n50
schema_description - No description provided in schema for parameter: QCReport.salmonella.max_n50
schema_description - No description provided in schema for parameter: QCReport.salmonella.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.salmonella.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.salmonella.min_length
schema_description - No description provided in schema for parameter: QCReport.salmonella.max_length
schema_description - No description provided in schema for parameter: QCReport.salmonella.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.salmonella.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.shigella.search
schema_description - No description provided in schema for parameter: QCReport.shigella.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.shigella.min_n50
schema_description - No description provided in schema for parameter: QCReport.shigella.max_n50
schema_description - No description provided in schema for parameter: QCReport.shigella.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.shigella.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.shigella.min_length
schema_description - No description provided in schema for parameter: QCReport.shigella.max_length
schema_description - No description provided in schema for parameter: QCReport.shigella.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.shigella.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.listeria.search
schema_description - No description provided in schema for parameter: QCReport.listeria.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.listeria.min_n50
schema_description - No description provided in schema for parameter: QCReport.listeria.max_n50
schema_description - No description provided in schema for parameter: QCReport.listeria.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.listeria.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.listeria.min_length
schema_description - No description provided in schema for parameter: QCReport.listeria.max_length
schema_description - No description provided in schema for parameter: QCReport.listeria.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.listeria.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.klebsiella.search
schema_description - No description provided in schema for parameter: QCReport.klebsiella.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.klebsiella.min_n50
schema_description - No description provided in schema for parameter: QCReport.klebsiella.max_n50
schema_description - No description provided in schema for parameter: QCReport.klebsiella.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.klebsiella.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.klebsiella.min_length
schema_description - No description provided in schema for parameter: QCReport.klebsiella.max_length
schema_description - No description provided in schema for parameter: QCReport.klebsiella.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.klebsiella.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.search
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.min_n50
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.max_n50
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.min_length
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.max_length
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.fallthrough.search
schema_description - No description provided in schema for parameter: QCReport.fallthrough.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.fallthrough.min_n50
schema_description - No description provided in schema for parameter: QCReport.fallthrough.max_n50
schema_description - No description provided in schema for parameter: QCReport.fallthrough.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.fallthrough.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.fallthrough.min_length
schema_description - No description provided in schema for parameter: QCReport.fallthrough.max_length
schema_description - No description provided in schema for parameter: QCReport.fallthrough.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.fallthrough.min_average_coverage
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.path
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.on
schema_description - No description provided in schema for parameter: QCReportFields.raw_average_quality.low_msg
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.path
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.on
schema_description - No description provided in schema for parameter: QCReportFields.average_coverage.low_msg
schema_description - No description provided in schema for parameter: QCReportFields.metagenomic.path
schema_description - No description provided in schema for parameter: QCReportFields.metagenomic.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.metagenomic.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.metagenomic.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.metagenomic.on
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.path
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.on
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.low_msg
schema_description - No description provided in schema for parameter: QCReportFields.n50_value.high_msg
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.path
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.on
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.low_msg
schema_description - No description provided in schema for parameter: QCReportFields.nr_contigs.high_msg
schema_description - No description provided in schema for parameter: QCReportFields.length.path
schema_description - No description provided in schema for parameter: QCReportFields.length.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.length.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.length.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.length.on
schema_description - No description provided in schema for parameter: QCReportFields.length.low_msg
schema_description - No description provided in schema for parameter: QCReportFields.length.high_msg
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.path
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.coerce_type
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.compare_fields
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.comp_type
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.on
schema_description - No description provided in schema for parameter: QCReportFields.checkm_contamination.high_msg
schema_description - No description provided in schema for parameter: QCReport.escherichia.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.salmonella.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.shigella.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.listeria.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.search
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.min_n50
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.max_n50
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.min_length
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.max_length
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.campylobacter_jejuni.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.search
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.min_n50
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.max_n50
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.min_length
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.max_length
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.campylobacter_coli.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.search
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.raw_average_quality
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.min_n50
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.max_n50
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.min_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.max_nr_contigs
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.min_length
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.max_length
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.max_checkm_contamination
schema_description - No description provided in schema for parameter: QCReport.vibrio_cholerae.min_average_coverage
schema_description - No description provided in schema for parameter: QCReport.klebsiella.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.staphylococcus.fixed_genome_size
schema_description - No description provided in schema for parameter: QCReport.fallthrough.fixed_genome_size
schema_description - No description provided in schema for parameter: seqtk_size.singularity
schema_description - No description provided in schema for parameter: seqtk_size.docker
schema_description - No description provided in schema for parameter: seqtk_size.report_tag
schema_description - No description provided in schema for parameter: medaka.fasta_ext
schema_description - No description provided in schema for parameter: medaka.outdir
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: mobsuite_recon.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: mobsuite_recon.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.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: 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: stage_in_mode
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.json_ext
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.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.args
schema_description - No description provided in schema for parameter: quast.contigs_field
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.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
files_exist - File is ignored: docs/output.md
files_exist - File is ignored: docs/README.md
files_exist - File is ignored: docs/usage.md
nextflow_config - nextflow_config
files_unchanged - File does not exist: CODE_OF_CONDUCT.md
files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/feature_request.yml
files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
files_unchanged - File ignored due to lint config: assets/email_template.html
files_unchanged - File ignored due to lint config: assets/email_template.txt
files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
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
files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/mikrokondo/mikrokondo/.github/workflows/awstest.yml
schema_params - schema_params
multiqc_config - multiqc_config

✅ Tests passed:

files_exist - File found: .gitattributes
files_exist - File found: .gitignore
files_exist - File found: .nf-core.yml
files_exist - File found: .editorconfig
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/branch.yml
files_exist - File found: .github/workflows/ci.yml
files_exist - File found: .github/workflows/linting_comment.yml
files_exist - File found: .github/workflows/linting.yml
files_exist - File found: assets/email_template.html
files_exist - File found: assets/email_template.txt
files_exist - File found: assets/sendmail_template.txt
files_exist - File found: conf/modules.config
files_exist - File found: conf/test.config
files_exist - File found: conf/test_full.config
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: 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: pipeline_template.yml
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: lib/Utils.groovy
files_exist - File not found check: lib/WorkflowMain.groovy
files_exist - File not found check: lib/NfcoreTemplate.groovy
files_exist - File not found check: lib/WorkflowMikrokondo.groovy
files_exist - File not found check: lib/nfcore_external_java_deps.jar
files_exist - File not found check: .travis.yml
files_unchanged - .gitattributes matches the template
files_unchanged - .prettierrc.yml matches the template
files_unchanged - .github/.dockstore.yml matches the template
files_unchanged - .github/workflows/linting_comment.yml matches the template
actions_ci - '.github/workflows/ci.yml' is triggered on expected events
actions_ci - '.github/workflows/ci.yml' checks minimum NF version
readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
pipeline_todos - No TODO strings found
pipeline_name_conventions - Name adheres to nf-core convention
template_strings - Did not find any Jinja template strings (181 files)
schema_lint - Schema lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
system_exit - No System.exit calls found
actions_schema_validation - Workflow validation passed: branch.yml
actions_schema_validation - Workflow validation passed: linting.yml
actions_schema_validation - Workflow validation passed: linting_comment.yml
actions_schema_validation - Workflow validation passed: doc.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
modules_structure - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL'

Run details

nf-core/tools version 2.13.1
Run at 2024-03-08 16:03:52

apetkau added 10 commits March 7, 2024 12:07

Added github linting tasks

8abdba1

Removed unneeded github actions

30035f8

Added template entry

7dd3fbc

Ran linter

ca46752

Ignoring many linting issues

d3d6888

Ignoring nearly errored linting now

ed2aa81

Revert dumpsoftwareversions back to version defined by commit

a4ffdfc

Removed some default values

f24c833

Added pre commit config

7e567e5

Ignore pre-commit

b36cfd0

apetkau changed the title ~~Add/linting~~ WIP:Add/linting Mar 7, 2024

apetkau marked this pull request as draft March 7, 2024 22:03

apetkau changed the title ~~WIP:Add/linting~~ Add/linting Mar 7, 2024

apetkau added 5 commits March 7, 2024 16:05

Added linting to files_unchanged

cb2f14d

Adjusted minimum nextflow version

e169209

Adjust nextflow badge in readme

9a63c0a

Enable pre-commit but adjust to only run on one file

e6edb11

Removed unneeded github action

d440e7b

apetkau marked this pull request as ready for review March 7, 2024 22:44

apetkau marked this pull request as draft March 7, 2024 22:51

Merge branch 'dev' into add/linting

aee9847

apetkau marked this pull request as ready for review March 8, 2024 16:06

apetkau requested a review from mattheww95 March 8, 2024 16:08

mattheww95 approved these changes Mar 8, 2024

View reviewed changes

apetkau merged commit f27fc49 into dev Mar 8, 2024
4 checks passed

apetkau deleted the add/linting branch March 8, 2024 16:10

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Add/linting #37

Add/linting #37

apetkau commented Mar 7, 2024 •

edited

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github-actions bot commented Mar 8, 2024 •

edited

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❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

Add/linting #37

Add/linting #37

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apetkau commented Mar 7, 2024 • edited Loading

github-actions bot commented Mar 8, 2024 • edited Loading

nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

Run details

apetkau commented Mar 7, 2024 •

edited

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github-actions bot commented Mar 8, 2024 •

edited

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