**TODO:** - Remove `.lint_skip` files wherever they are not necessary - Resolve all linting issues - Prefer IUC standards where applicable --- - [x] [abricate](https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7946 - [x] [adapter_removal](https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal/.lint_skip) - [x] [add_input_name_as_column](https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7964 - [x] [aegean](https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean/.lint_skip) - [x] [aldex2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2/.lint_skip) - [x] [allegro](https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7965 - [x] [ampvis2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7418 - [x] [amrfinderplus](https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7939 - [ ] [anndata2ri](https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri/.lint_skip) - [ ] [arriba](https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba/.lint_skip) - [ ] [art](https://github.com/galaxyproject/tools-iuc/tree/main/tools/art/.lint_skip) - [ ] [artic](https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic/.lint_skip) - [ ] [b2btools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools/.lint_skip) - [ ] [bamutil](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil/.lint_skip) - [ ] [bandage](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage/.lint_skip) - [ ] [barcode_splitter](https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter/.lint_skip) - [ ] [baredsc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc/.lint_skip) - [ ] [bayescan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan/.lint_skip) - [ ] [bbtools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools/.lint_skip) - [ ] [bcftools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools/.lint_skip) - [ ] [beacon2-import](https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import/.lint_skip) - [ ] [beagle](https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle/.lint_skip) - [x] [bedtools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7940 - [ ] [bigscape](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape/.lint_skip) - [ ] [bigwig_outlier_bed](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed/.lint_skip) - [ ] [bioext](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext/.lint_skip) - [ ] [bioinformatics_cafe](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe/.lint_skip) - [x] [biom_format](https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7966 - [ ] [blast](https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast/.lint_skip) - [ ] [blastxml_to_gapped_gff3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3/.lint_skip) - [ ] [breseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq/.lint_skip) - [ ] [bwa](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa/.lint_skip) - [ ] [bwa_mem2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2/.lint_skip) - [ ] [cat](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat/.lint_skip) - [ ] [cdhit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit/.lint_skip) - [ ] [charts](https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts/.lint_skip) - [x] [checkm2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7941 - [ ] [cherri](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri/.lint_skip) - [ ] [chira](https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira/.lint_skip) - [ ] [chromeister](https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister/.lint_skip) - [ ] [circos](https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos/.lint_skip) - [ ] [cite_seq_count](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count/.lint_skip) - [ ] [clustalw](https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw/.lint_skip) - [ ] [cnvkit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit/.lint_skip) - [ ] [codeml](https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml/.lint_skip) - [ ] [cojac](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac/.lint_skip) - [ ] [colabfold](https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold/.lint_skip) - [ ] [colibread](https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread/.lint_skip) - [ ] [collection_column_join](https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join/.lint_skip) - [ ] [collection_element_identifiers](https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers/.lint_skip) - [ ] [column_maker](https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker/.lint_skip) - [ ] [column_order_header_sort](https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort/.lint_skip) - [ ] [column_remove_by_header](https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header/.lint_skip) - [ ] [compress_file](https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file/.lint_skip) - [ ] [concoct](https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/8007 - [ ] [cosg](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg/.lint_skip) - [ ] [coverm](https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm/.lint_skip) - [ ] [crispr_studio](https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio/.lint_skip) - [ ] [crossmap](https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap/.lint_skip) - [ ] [cutadapt](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt/.lint_skip) - [ ] [cwpair2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2/.lint_skip) - [ ] [decontaminator](https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator/.lint_skip) - [ ] [deepmicro](https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro/.lint_skip) - [ ] [deg_annotate](https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate/.lint_skip) - [ ] [delly](https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly/.lint_skip) - [ ] [deseq2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2/.lint_skip) - [ ] [detect_circular_sequences](https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences/.lint_skip) - [ ] [dexseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq/.lint_skip) - [ ] [diffbind](https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind/.lint_skip) - [ ] [dimet](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet/.lint_skip) - [ ] [disco](https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco/.lint_skip) - [ ] [dnaweaver](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver/.lint_skip) - [ ] [dram](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram/.lint_skip) - [ ] [drep](https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep/.lint_skip) - [ ] [dropletutils](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils/.lint_skip) - [ ] [egsea](https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea/.lint_skip) - [ ] [emboss_5](https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5/.lint_skip) - [ ] [enasearch](https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch/.lint_skip) - [ ] [ena_upload](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload/.lint_skip) - [ ] [ensembl_vep](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep/.lint_skip) - [ ] [episcanpy](https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy/.lint_skip) - [ ] [ete-toolkit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit/.lint_skip) - [ ] [exonerate](https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate/.lint_skip) - [ ] [export2graphlan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan/.lint_skip) - [ ] [extract_genomic_dna](https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna/.lint_skip) - [ ] [fairy](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy/.lint_skip) - [ ] [falco](https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco/.lint_skip) - [ ] [fargene](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene/.lint_skip) - [ ] [fasplit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit/.lint_skip) - [ ] [fasta_nucleotide_color_plot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot/.lint_skip) - [ ] [fastk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk/.lint_skip) - [ ] [fastqc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc/.lint_skip) - [ ] [fasttree](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree/.lint_skip) - [ ] [featurecounts](https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts/.lint_skip) - [ ] [fermikit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit/.lint_skip) - [ ] [fgsea](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea/.lint_skip) - [ ] [flair](https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair/.lint_skip) - [ ] [flash](https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash/.lint_skip) - [ ] [fraggenescan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan/.lint_skip) - [ ] [freebayes](https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes/.lint_skip) - [ ] [freec](https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec/.lint_skip) - [ ] [freyja](https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja/.lint_skip) - [ ] [gatk4](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4/.lint_skip) - [ ] [gemini](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini/.lint_skip) - [ ] [gem_tools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools/.lint_skip) - [ ] [genebed_maf_to_fasta](https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta/.lint_skip) - [ ] [genehunter_modscore](https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore/.lint_skip) - [ ] [geneiobio](https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio/.lint_skip) - [ ] [genetrack](https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack/.lint_skip) - [ ] [genomic_super_signature](https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature/.lint_skip) - [ ] [genrich](https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich/.lint_skip) - [ ] [getorganelle](https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle/.lint_skip) - [ ] [gfa_to_fa](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa/.lint_skip) - [ ] [gffread](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread/.lint_skip) - [ ] [ggplot2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2/.lint_skip) - [ ] [ggupset](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset/.lint_skip) - [ ] [glimmer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer/.lint_skip) - [ ] [goenrichment](https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment/.lint_skip) - [ ] [goseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq/.lint_skip) - [ ] [gprofiler](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler/.lint_skip) - [ ] [graphembed](https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed/.lint_skip) - [ ] [graphlan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan/.lint_skip) - [ ] [gtfToBed12](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12/.lint_skip) - [ ] [gubbins](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins/.lint_skip) - [ ] [gvcftools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools/.lint_skip) - [ ] [gwastools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwastools/.lint_skip) - [ ] [hansel](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel/.lint_skip) - [ ] [hapcut2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2/.lint_skip) - [ ] [heatmap2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2/.lint_skip) - [ ] [heinz](https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz/.lint_skip) - [ ] [hicexplorer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer/.lint_skip) - [ ] [hifiasm](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm/.lint_skip) - [ ] [hifiasm_meta](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta/.lint_skip) - [ ] [hisat2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2/.lint_skip) - [ ] [hmmer3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3/.lint_skip) - [ ] [homer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer/.lint_skip) - [ ] [htseq_count](https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count/.lint_skip) - [ ] [humann](https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann/.lint_skip) - [ ] [hybpiper](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper/.lint_skip) - [ ] [hypo](https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo/.lint_skip) - [ ] [icescreen](https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen/.lint_skip) - [ ] [idba_ud](https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud/.lint_skip) - [x] [idr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7943 - [ ] [idr_download](https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7944 - [ ] [interproscan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan/.lint_skip) - [ ] [interval2maf](https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf/.lint_skip) - [ ] [intervene](https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene/.lint_skip) - [x] [iqtree](https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/4724 - [ ] [isoformswitchanalyzer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer/.lint_skip) - [ ] [ivar](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar/.lint_skip) - [ ] [iwtomics](https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics/.lint_skip) - [ ] [jbrowse](https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse/.lint_skip) - [ ] [jellyfish](https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish/.lint_skip) - [ ] [join_files_by_id](https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id/.lint_skip) - [ ] [jvarkit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit/.lint_skip) - [ ] [kallisto](https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto/.lint_skip) - [ ] [kc-align](https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align/.lint_skip) - [ ] [khmer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer/.lint_skip) - [ ] [king](https://github.com/galaxyproject/tools-iuc/tree/main/tools/king/.lint_skip) - [ ] [kleborate](https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate/.lint_skip) - [ ] [kofamscan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan/.lint_skip) - [ ] [krakentools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools/.lint_skip) - [ ] [krocus](https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus/.lint_skip) - [ ] [lcrgenie](https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie/.lint_skip) - [ ] [length_and_gc_content](https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content/.lint_skip) - [ ] [limma_voom](https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom/.lint_skip) - [ ] [links](https://github.com/galaxyproject/tools-iuc/tree/main/tools/links/.lint_skip) - [ ] [lofreq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq/.lint_skip) - [ ] [lorikeet](https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet/.lint_skip) - [ ] [macs2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2/.lint_skip) - [ ] [maf_stats](https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats/.lint_skip) - [ ] [maftoaxt](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt/.lint_skip) - [ ] [mageck](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck/.lint_skip) - [ ] [maker](https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker/.lint_skip) - [ ] [malt](https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt/.lint_skip) - [ ] [map_param_value](https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value/.lint_skip) - [ ] [mapseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq/.lint_skip) - [ ] [masigpro](https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro/.lint_skip) - [ ] [maxbin2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2/.lint_skip) - [ ] [mcl](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl/.lint_skip) - [ ] [megahit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit/.lint_skip) - [ ] [megahit_contig2fastg](https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg/.lint_skip) - [ ] [megan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan/.lint_skip) - [ ] [meme](https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme/.lint_skip) - [ ] [meme_chip](https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip/.lint_skip) - [ ] [merlin](https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin/.lint_skip) - [ ] [merquryfk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk/.lint_skip) - [ ] [meryl](https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl/.lint_skip) - [x] [metabat2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7962 - [ ] [metabuli](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli/.lint_skip) - [ ] [metaeuk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk/.lint_skip) - [ ] [metagenomeseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq/.lint_skip) - [ ] [metawrapmg](https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg/.lint_skip) - [ ] [mg_toolkit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit/.lint_skip) - [ ] [migmap](https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap/.lint_skip) - [ ] [minia](https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia/.lint_skip) - [ ] [miniasm](https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm/.lint_skip) - [ ] [miniprot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot/.lint_skip) - [ ] [mirnature](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature/.lint_skip) - [ ] [mlst](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst/.lint_skip) - [ ] [mmseqs2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2/.lint_skip) - [ ] [moabs](https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs/.lint_skip) - [ ] [mothur](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur/.lint_skip) - [ ] [msaboot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot/.lint_skip) - [ ] [multigps](https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps/.lint_skip) - [ ] [multigsea](https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea/.lint_skip) - [ ] [multiqc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc/.lint_skip) - [ ] [mummer4](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4/.lint_skip) - [ ] [muon](https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon/.lint_skip) - [ ] [mykrobe](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe/.lint_skip) - [ ] [mzmine](https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine/.lint_skip) - [ ] [naltorfs](https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs/.lint_skip) - [ ] [nanocompore](https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore/.lint_skip) - [ ] [nanoplot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot/.lint_skip) - [ ] [ncbi_acc_download](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download/.lint_skip) - [ ] [ncbi_entrez_eutils](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils/.lint_skip) - [ ] [ncbi_fcs_gx](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx/.lint_skip) - [ ] [necat](https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat/.lint_skip) - [ ] [newick_utils](https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils/.lint_skip) - [ ] [ngmlr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr/.lint_skip) - [ ] [ngsutils](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils/.lint_skip) - [ ] [nonpareil](https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil/.lint_skip) - [ ] [novoplasty](https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty/.lint_skip) - [x] [obitools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools/.lint_skip) - [ ] [ococo](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo/.lint_skip) - [ ] [odgi](https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi/.lint_skip) - [ ] [omark](https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark/.lint_skip) - [ ] [packaged_annotation_loader](https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader/.lint_skip) - [ ] [pathview](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview/.lint_skip) - [ ] [pbgcpp](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp/.lint_skip) - [ ] [pbtk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk/.lint_skip) - [ ] [peakzilla](https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla/.lint_skip) - [ ] [pear](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear/.lint_skip) - [ ] [phyloseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq/.lint_skip) - [ ] [phyml](https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml/.lint_skip) - [ ] [picard](https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard/.lint_skip) - [ ] [picrust](https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust/.lint_skip) - [ ] [picrust2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2/.lint_skip) - [ ] [pilon](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon/.lint_skip) - [ ] [pizzly](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly/.lint_skip) - [ ] [plink](https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink/.lint_skip) - [ ] [polypolish](https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish/.lint_skip) - [ ] [porechop](https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop/.lint_skip) - [ ] [poretools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools/.lint_skip) - [ ] [ppanggolin](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin/.lint_skip) - [ ] [presto](https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto/.lint_skip) - [ ] [prinseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq/.lint_skip) - [ ] [progressivemauve](https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve/.lint_skip) - [ ] [prokka](https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka/.lint_skip) - [ ] [proteinortho](https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho/.lint_skip) - [ ] [prot-scriber](https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber/.lint_skip) - [ ] [pureclip](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip/.lint_skip) - [ ] [pyega3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3/.lint_skip) - [ ] [pygenometracks](https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks/.lint_skip) - [ ] [qfilt](https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt/.lint_skip) - [ ] [qiime_add_on](https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on/.lint_skip) - [ ] [qiime_core](https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core/.lint_skip) - [ ] [quast](https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast/.lint_skip) - [ ] [query_impc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc/.lint_skip) - [ ] [query_tabular](https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular/.lint_skip) - [ ] [quickmerge](https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge/.lint_skip) - [ ] [quicktree](https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree/.lint_skip) - [ ] [raceid](https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid/.lint_skip) - [ ] [rapidnj](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj/.lint_skip) - [ ] [rasusa](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa/.lint_skip) - [ ] [raxml](https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml/.lint_skip) - [ ] [rcorrector](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector/.lint_skip) - [ ] [read_it_and_keep](https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep/.lint_skip) - [ ] [recentrifuge](https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge/.lint_skip) - [ ] [repeatmasker](https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker/.lint_skip) - [ ] [repmatch_gff3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3/.lint_skip) - [ ] [rgrnastar](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar/.lint_skip) - [ ] [ribowaltz](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz/.lint_skip) - [ ] [roary](https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary/.lint_skip) - [ ] [rp2biosensor](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor/.lint_skip) - [ ] [rpbasicdesign](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign/.lint_skip) - [ ] [rptools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools/.lint_skip) - [ ] [rseqc](https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc/.lint_skip) - [ ] [ruvseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq/.lint_skip) - [ ] [sbml2sbol](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol/.lint_skip) - [ ] [scater](https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater/.lint_skip) - [ ] [sceasy](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy/.lint_skip) - [ ] [scpipe](https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe/.lint_skip) - [ ] [seacr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr/.lint_skip) - [ ] [seqcomplexity](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity/.lint_skip) - [ ] [seqprep](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep/.lint_skip) - [ ] [seqsero2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2/.lint_skip) - [ ] [seqtk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk/.lint_skip) - [ ] [seqwish](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish/.lint_skip) - [ ] [seurat](https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat/.lint_skip) - [ ] [shasta](https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta/.lint_skip) - [ ] [shorah](https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah/.lint_skip) - [ ] [sickle](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle/.lint_skip) - [ ] [simtext](https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext/.lint_skip) - [ ] [sina](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina/.lint_skip) - [ ] [sinto](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto/.lint_skip) - [ ] [slamdunk](https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk/.lint_skip) - [ ] [sleuth](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth/.lint_skip) - [ ] [smudgeplot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot/.lint_skip) - [ ] [snap](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap/.lint_skip) - [ ] [sniffles](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles/.lint_skip) - [ ] [snipit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit/.lint_skip) - [ ] [snippy](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy/.lint_skip) - [ ] [snp-dists](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists/.lint_skip) - [ ] [snpeff-covid19](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19/.lint_skip) - [ ] [snpfreqplot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot/.lint_skip) - [ ] [snp-sites](https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites/.lint_skip) - [ ] [sonneityping](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping/.lint_skip) - [ ] [spacexr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr/.lint_skip) - [ ] [spaln](https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln/.lint_skip) - [ ] [spapros](https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros/.lint_skip) - [ ] [spotyping](https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping/.lint_skip) - [ ] [squirrel](https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel/.lint_skip) - [ ] [sra-tools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools/.lint_skip) - [ ] [stacks](https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks/.lint_skip) - [ ] [stacks2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2/.lint_skip) - [x] [staramr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr/.lint_skip) https://github.com/galaxyproject/tools-iuc/pull/7942 - [ ] [star_fusion](https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion/.lint_skip) - [ ] [straindesign](https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign/.lint_skip) - [ ] [strelka](https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka/.lint_skip) - [ ] [stringtie](https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie/.lint_skip) - [ ] [structure](https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure/.lint_skip) - [ ] [swift](https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift/.lint_skip) - [ ] [table_compute](https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute/.lint_skip) - [ ] [tag_pileup_frequency](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency/.lint_skip) - [ ] [tasmanian_mismatch](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch/.lint_skip) - [ ] [taxonomy_filter_refseq](https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq/.lint_skip) - [ ] [taxonomy_krona_chart](https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart/.lint_skip) - [ ] [tbl2gff3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3/.lint_skip) - [ ] [te_finder](https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder/.lint_skip) - [ ] [telescope](https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope/.lint_skip) - [ ] [tn93](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93/.lint_skip) - [ ] [tracegroomer](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer/.lint_skip) - [ ] [transdecoder](https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder/.lint_skip) - [ ] [transit](https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit/.lint_skip) - [ ] [transtermhp](https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp/.lint_skip) - [ ] [trimmomatic](https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic/.lint_skip) - [ ] [trinity](https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity/.lint_skip) - [ ] [trinotate](https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate/.lint_skip) - [ ] [trycycler](https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler/.lint_skip) - [ ] [tsne](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne/.lint_skip) - [ ] [tximport](https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport/.lint_skip) - [ ] [ucsc_blat](https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat/.lint_skip) - [ ] [umi_tools](https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools/.lint_skip) - [ ] [unicycler](https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler/.lint_skip) - [ ] [upsetr](https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr/.lint_skip) - [ ] [usher](https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher/.lint_skip) - [ ] [valet](https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet/.lint_skip) - [ ] [varscan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan/.lint_skip) - [ ] [vcf2maf](https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf/.lint_skip) - [ ] [vegan](https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan/.lint_skip) - [ ] [verkko](https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko/.lint_skip) - [ ] [vg](https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg/.lint_skip) - [ ] [virheat](https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat/.lint_skip) - [ ] [volcanoplot](https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot/.lint_skip) - [ ] [vsearch](https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch/.lint_skip) - [ ] [vsnp](https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp/.lint_skip) - [ ] [weblogo3](https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3/.lint_skip) - [ ] [windowmasker](https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker/.lint_skip) - [ ] [winnowmap](https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap/.lint_skip) - [ ] [xpath](https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath/.lint_skip) - [ ] [yahs](https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs/.lint_skip)
TODO:
.lint_skipfiles wherever they are not necessary