From f725af85f8025eac8c3cacb66f6560ee83597400 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Sat, 27 Jul 2024 19:59:31 +0200 Subject: [PATCH 01/15] add linter exceptions for all linters that are currently failing --- .github/workflows/ci.yaml | 5 +++-- .github/workflows/pr.yaml | 11 +---------- .../data_manager_bowtie2_index_builder/.lint_skip | 2 ++ .../data_manager_bowtie_index_builder/.lint_skip | 1 + data_managers/data_manager_build_kma_index/.lint_skip | 1 + .../data_manager_build_kraken_database/.lint_skip | 2 ++ .../data_manager_bwa_mem_index_builder/.lint_skip | 1 + .../data_manager_fetch_gene_annotation/.lint_skip | 3 +++ .../.lint_skip | 1 + data_managers/data_manager_fetch_index_maf/.lint_skip | 2 ++ .../data_manager_fetch_ncbi_taxonomy/.lint_skip | 1 + .../data_manager_gatk_picard_index_builder/.lint_skip | 2 ++ .../.lint_skip | 1 + .../data_manager_gtdbtk_database_installer/.lint_skip | 1 + data_managers/data_manager_homer_preparsed/.lint_skip | 3 +++ .../data_manager_kallisto_index_builder/.lint_skip | 2 ++ .../data_manager_malt_index_builder/.lint_skip | 1 + data_managers/data_manager_manual/.lint_skip | 3 +++ .../data_manager_mash_sketch_builder/.lint_skip | 1 + .../data_manager_mothur_toolsuite/.lint_skip | 1 + .../data_manager_packaged_annotation_data/.lint_skip | 1 + data_managers/data_manager_pangolin_data/.lint_skip | 2 ++ .../data_manager_picard_index_builder/.lint_skip | 1 + .../data_manager_qiime_database_downloader/.lint_skip | 1 + .../data_manager_salmon_index_builder/.lint_skip | 1 + .../data_manager_sam_fasta_index_builder/.lint_skip | 1 + .../data_manager_selection_background/.lint_skip | 2 ++ data_managers/data_manager_semibin/.lint_skip | 1 + data_managers/data_manager_snpeff/.lint_skip | 2 ++ .../data_manager_star_index_builder/.lint_skip | 1 + data_managers/data_manager_twobit_builder/.lint_skip | 2 ++ data_managers/data_manager_vsnp_dnaprints/.lint_skip | 1 + data_managers/data_manager_vsnp_excel/.lint_skip | 1 + data_managers/data_manager_vsnp_genbank/.lint_skip | 1 + tool_collections/cufflinks/cuffdiff/.lint_skip | 1 + tool_collections/cufflinks/cuffnorm/.lint_skip | 2 ++ .../fastx_toolkit/fastx_clipper/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_combiner/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_filter/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_groomer/.lint_skip | 1 + .../fastq_manipulation/.lint_skip | 1 + .../fastq_masker_by_quality/.lint_skip | 1 + .../fastq_paired_end_deinterlacer/.lint_skip | 1 + .../fastq_paired_end_interlacer/.lint_skip | 3 +++ .../fastq_paired_end_joiner/.lint_skip | 1 + .../fastq_paired_end_splitter/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_stats/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_to_tabular/.lint_skip | 1 + .../galaxy_sequence_utils/fastq_trimmer/.lint_skip | 1 + .../galaxy_sequence_utils/fastqtofasta/.lint_skip | 1 + .../galaxy_sequence_utils/tabular_to_fastq/.lint_skip | 1 + tool_collections/snpeff/.lint_skip | 3 +++ tool_collections/snpsift/snpsift/.lint_skip | 2 ++ tool_collections/snpsift/snpsift_dbnsfp/.lint_skip | 1 + tool_collections/snpsift/snpsift_genesets/.lint_skip | 1 + tool_collections/vcflib/vcffilter/.lint_skip | 1 + tool_collections/vcflib/vcfsort/.lint_skip | 1 + tools/abricate/.lint_skip | 2 ++ tools/add_input_name_as_column/.lint_skip | 1 + tools/allegro/.lint_skip | 1 + tools/amplican/.lint_skip | 1 + tools/arriba/.lint_skip | 1 + tools/art/.lint_skip | 4 ++++ tools/augustus/.lint_skip | 5 +++++ tools/b2btools/.lint_skip | 1 + tools/bamutil/.lint_skip | 2 ++ tools/barcode_splitter/.lint_skip | 2 ++ tools/baredsc/.lint_skip | 1 + tools/barrnap/.lint_skip | 1 + tools/bctools/.lint_skip | 3 +++ tools/beagle/.lint_skip | 1 + tools/bioperl/.lint_skip | 1 + tools/blastxml_to_gapped_gff3/.lint_skip | 1 + tools/bowtie2/.lint_skip | 1 + tools/breseq/.lint_skip | 3 +++ tools/bwa/.lint_skip | 1 + tools/bwa_mem2/.lint_skip | 2 ++ tools/cat/.lint_skip | 2 ++ tools/cdhit/.lint_skip | 1 + tools/charts/.lint_skip | 2 ++ tools/checkm/.lint_skip | 2 ++ tools/cherri/.lint_skip | 1 + tools/chira/.lint_skip | 1 + tools/circexplorer2/.lint_skip | 1 + tools/circos/.lint_skip | 1 + tools/cite_seq_count/.lint_skip | 1 + tools/colibread/.lint_skip | 3 +++ tools/collection_column_join/.lint_skip | 3 +++ tools/collection_element_identifiers/.lint_skip | 1 + tools/column_maker/.lint_skip | 1 + tools/column_order_header_sort/.lint_skip | 1 + tools/column_remove_by_header/.lint_skip | 1 + tools/compress_file/.lint_skip | 1 + tools/crossmap/.lint_skip | 1 + tools/cutesv/.lint_skip | 2 ++ tools/cwpair2/.lint_skip | 1 + tools/decontaminator/.lint_skip | 1 + tools/deg_annotate/.lint_skip | 1 + tools/delly/.lint_skip | 1 + tools/diamond/.lint_skip | 2 ++ tools/disco/.lint_skip | 4 ++++ tools/dnaweaver/.lint_skip | 1 + tools/dropletutils/.lint_skip | 1 + tools/emboss_5/.lint_skip | 6 ++++++ tools/exonerate/.lint_skip | 2 ++ tools/extract_genomic_dna/.lint_skip | 1 + tools/fasta_nucleotide_color_plot/.lint_skip | 1 + tools/fasttree/.lint_skip | 4 ++++ tools/fermikit/.lint_skip | 1 + tools/fgsea/.lint_skip | 1 + tools/flair/.lint_skip | 1 + tools/flash/.lint_skip | 4 ++++ tools/fraggenescan/.lint_skip | 1 + tools/freebayes/.lint_skip | 3 +++ tools/gatk4/.lint_skip | 5 +++++ tools/gecko/.lint_skip | 1 + tools/gemini/.lint_skip | 5 +++++ tools/genehunter_modscore/.lint_skip | 1 + tools/genomic_super_signature/.lint_skip | 1 + tools/gfa_to_fa/.lint_skip | 1 + tools/gffcompare/.lint_skip | 2 ++ tools/ggplot2/.lint_skip | 4 ++++ tools/ggupset/.lint_skip | 1 + tools/glimmer/.lint_skip | 5 +++++ tools/goenrichment/.lint_skip | 1 + tools/goseq/.lint_skip | 1 + tools/gprofiler/.lint_skip | 1 + tools/gvcftools/.lint_skip | 1 + tools/hansel/.lint_skip | 1 + tools/happy/.lint_skip | 1 + tools/hicstuff/.lint_skip | 1 + tools/hisat2/.lint_skip | 2 ++ tools/hivclustering/.lint_skip | 2 ++ tools/hybpiper/.lint_skip | 1 + tools/hyphy/.lint_skip | 1 + tools/hypo/.lint_skip | 1 + tools/idba_ud/.lint_skip | 1 + tools/idr/.lint_skip | 2 ++ tools/idr_download/.lint_skip | 1 + tools/iedb_api/.lint_skip | 2 ++ tools/intermine_galaxy_exchange/.lint_skip | 1 + tools/interproscan/.lint_skip | 2 ++ tools/intervene/.lint_skip | 1 + tools/iwtomics/.lint_skip | 1 + tools/jbrowse/.lint_skip | 3 +++ tools/jellyfish/.lint_skip | 1 + tools/join_files_by_id/.lint_skip | 1 + tools/jq/.lint_skip | 1 + tools/jvarkit/.lint_skip | 1 + tools/kallisto/.lint_skip | 1 + tools/khmer/.lint_skip | 5 +++++ tools/king/.lint_skip | 1 + tools/krakentools/.lint_skip | 1 + tools/lcrgenie/.lint_skip | 1 + tools/length_and_gc_content/.lint_skip | 1 + tools/links/.lint_skip | 2 ++ tools/lofreq/.lint_skip | 2 ++ tools/mageck/.lint_skip | 3 +++ tools/maker/.lint_skip | 2 ++ tools/malt/.lint_skip | 1 + tools/map_param_value/.lint_skip | 1 + tools/mash/.lint_skip | 1 + tools/masigpro/.lint_skip | 2 ++ tools/megahit_contig2fastg/.lint_skip | 1 + tools/megan/.lint_skip | 2 ++ tools/meme/.lint_skip | 3 +++ tools/merlin/.lint_skip | 1 + tools/metaeuk/.lint_skip | 4 ++++ tools/metagenomeseq/.lint_skip | 2 ++ tools/migmap/.lint_skip | 1 + tools/minia/.lint_skip | 1 + tools/mirnature/.lint_skip | 2 ++ tools/mlst/.lint_skip | 2 ++ tools/moabs/.lint_skip | 1 + tools/mothur/.lint_skip | 5 +++++ tools/msaboot/.lint_skip | 2 ++ tools/multigps/.lint_skip | 1 + tools/mummer4/macros.xml | 2 +- tools/mykrobe/.lint_skip | 1 + tools/mzmine/.lint_skip | 1 + tools/naltorfs/.lint_skip | 1 + tools/nanocompore/.lint_skip | 1 + tools/ncbi_acc_download/.lint_skip | 2 ++ tools/ncbi_entrez_eutils/.lint_skip | 2 ++ tools/necat/.lint_skip | 1 + tools/newick_utils/.lint_skip | 1 + tools/ngmlr/.lint_skip | 1 + tools/ngsutils/.lint_skip | 2 ++ tools/ococo/.lint_skip | 2 ++ tools/odgi/.lint_skip | 2 ++ tools/packaged_annotation_loader/.lint_skip | 1 + tools/pathview/.lint_skip | 2 ++ tools/pbgcpp/.lint_skip | 2 ++ tools/pe_histogram/.lint_skip | 1 + tools/picard/.lint_skip | 1 + tools/picrust2/.lint_skip | 1 + tools/pilon/.lint_skip | 2 ++ tools/pizzly/.lint_skip | 1 + tools/plink/.lint_skip | 1 + tools/porechop/.lint_skip | 1 + tools/poretools/.lint_skip | 7 +++++++ tools/presto/.lint_skip | 4 ++++ tools/prinseq/.lint_skip | 2 ++ tools/progressivemauve/.lint_skip | 3 +++ tools/prokka/.lint_skip | 2 ++ tools/pureclip/.lint_skip | 1 + tools/quickmerge/.lint_skip | 1 + tools/raceid/.lint_skip | 1 + tools/rapidnj/.lint_skip | 2 ++ tools/rcorrector/.lint_skip | 2 ++ tools/repeatmasker/.lint_skip | 2 ++ tools/repmatch_gff3/.lint_skip | 1 + tools/ribowaltz/.lint_skip | 1 + tools/roary/.lint_skip | 1 + tools/rp2biosensor/.lint_skip | 1 + tools/rptools/.lint_skip | 1 + tools/rrparser/.lint_skip | 1 + tools/ruvseq/.lint_skip | 2 ++ tools/salsa2/.lint_skip | 1 + tools/samblaster/.lint_skip | 2 ++ tools/sbml2sbol/.lint_skip | 1 + tools/scater/.lint_skip | 2 ++ tools/scpipe/.lint_skip | 1 + tools/seqcomplexity/.lint_skip | 1 + tools/seqwish/.lint_skip | 1 + tools/shorah/.lint_skip | 2 ++ tools/sickle/.lint_skip | 2 ++ tools/simtext/.lint_skip | 1 + tools/sina/.lint_skip | 2 ++ tools/slamdunk/.lint_skip | 1 + tools/snap/.lint_skip | 3 +++ tools/sniffles/.lint_skip | 2 ++ tools/snippy/.lint_skip | 3 +++ tools/snp-dists/.lint_skip | 1 + tools/snpeff-covid19/.lint_skip | 3 +++ tools/snpfreqplot/.lint_skip | 1 + tools/spaln/.lint_skip | 1 + tools/spotyping/.lint_skip | 1 + tools/stacks/.lint_skip | 1 + tools/stacks2/.lint_skip | 3 +++ tools/star_fusion/.lint_skip | 1 + tools/strelka/.lint_skip | 1 + tools/structure/.lint_skip | 1 + tools/structureharvester/.lint_skip | 2 ++ tools/swift/.lint_skip | 2 ++ tools/table_compute/.lint_skip | 2 ++ tools/tag_pileup_frequency/.lint_skip | 1 + tools/tasmanian_mismatch/.lint_skip | 1 + tools/tbl2gff3/.lint_skip | 1 + tools/telescope/.lint_skip | 3 +++ tools/tetyper/.lint_skip | 1 + tools/tn93/.lint_skip | 2 ++ tools/transdecoder/.lint_skip | 1 + tools/transit/.lint_skip | 1 + tools/trinotate/.lint_skip | 2 ++ tools/tsne/.lint_skip | 1 + tools/tximport/.lint_skip | 1 + tools/ucsc_blat/.lint_skip | 1 + tools/ucsc_tools/fasplit/.lint_skip | 2 ++ tools/ucsc_tools/twobittofa/.lint_skip | 2 ++ tools/umi_tools/.lint_skip | 6 ++++++ tools/varscan/.lint_skip | 1 + tools/vcf2maf/.lint_skip | 1 + tools/velvet/.lint_skip | 1 + tools/vg/.lint_skip | 2 ++ tools/vsearch/.lint_skip | 3 +++ tools/vsnp/.lint_skip | 1 + tools/winnowmap/.lint_skip | 1 + tools/xpath/.lint_skip | 1 + 269 files changed, 436 insertions(+), 13 deletions(-) create mode 100644 data_managers/data_manager_bowtie2_index_builder/.lint_skip create mode 100644 data_managers/data_manager_bowtie_index_builder/.lint_skip create mode 100644 data_managers/data_manager_build_kma_index/.lint_skip create mode 100644 data_managers/data_manager_build_kraken_database/.lint_skip create mode 100644 data_managers/data_manager_bwa_mem_index_builder/.lint_skip create mode 100644 data_managers/data_manager_fetch_gene_annotation/.lint_skip create mode 100644 data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip create mode 100644 data_managers/data_manager_fetch_index_maf/.lint_skip create mode 100644 data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip create mode 100644 data_managers/data_manager_gatk_picard_index_builder/.lint_skip create mode 100644 data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip create mode 100644 data_managers/data_manager_gtdbtk_database_installer/.lint_skip create mode 100644 data_managers/data_manager_homer_preparsed/.lint_skip create mode 100644 data_managers/data_manager_kallisto_index_builder/.lint_skip create mode 100644 data_managers/data_manager_malt_index_builder/.lint_skip create mode 100644 data_managers/data_manager_manual/.lint_skip create mode 100644 data_managers/data_manager_mash_sketch_builder/.lint_skip create mode 100644 data_managers/data_manager_mothur_toolsuite/.lint_skip create mode 100644 data_managers/data_manager_packaged_annotation_data/.lint_skip create mode 100644 data_managers/data_manager_pangolin_data/.lint_skip create mode 100644 data_managers/data_manager_picard_index_builder/.lint_skip create mode 100644 data_managers/data_manager_qiime_database_downloader/.lint_skip create mode 100644 data_managers/data_manager_salmon_index_builder/.lint_skip create mode 100644 data_managers/data_manager_sam_fasta_index_builder/.lint_skip create mode 100644 data_managers/data_manager_selection_background/.lint_skip create mode 100644 data_managers/data_manager_semibin/.lint_skip create mode 100644 data_managers/data_manager_snpeff/.lint_skip create mode 100644 data_managers/data_manager_star_index_builder/.lint_skip create mode 100644 data_managers/data_manager_twobit_builder/.lint_skip create mode 100644 data_managers/data_manager_vsnp_dnaprints/.lint_skip create mode 100644 data_managers/data_manager_vsnp_excel/.lint_skip create mode 100644 data_managers/data_manager_vsnp_genbank/.lint_skip create mode 100644 tool_collections/cufflinks/cuffdiff/.lint_skip create mode 100644 tool_collections/cufflinks/cuffnorm/.lint_skip create mode 100644 tool_collections/fastx_toolkit/fastx_clipper/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip create mode 100644 tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip create mode 100644 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100644 tools/allegro/.lint_skip create mode 100644 tools/amplican/.lint_skip create mode 100644 tools/arriba/.lint_skip create mode 100644 tools/art/.lint_skip create mode 100644 tools/augustus/.lint_skip create mode 100644 tools/b2btools/.lint_skip create mode 100644 tools/bamutil/.lint_skip create mode 100644 tools/barcode_splitter/.lint_skip create mode 100644 tools/baredsc/.lint_skip create mode 100644 tools/barrnap/.lint_skip create mode 100644 tools/bctools/.lint_skip create mode 100644 tools/beagle/.lint_skip create mode 100644 tools/bioperl/.lint_skip create mode 100644 tools/blastxml_to_gapped_gff3/.lint_skip create mode 100644 tools/bowtie2/.lint_skip create mode 100644 tools/breseq/.lint_skip create mode 100644 tools/bwa/.lint_skip create mode 100644 tools/bwa_mem2/.lint_skip create mode 100644 tools/cat/.lint_skip create mode 100644 tools/cdhit/.lint_skip create mode 100644 tools/charts/.lint_skip create mode 100644 tools/checkm/.lint_skip create mode 100644 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tools/snp-dists/.lint_skip create mode 100644 tools/snpeff-covid19/.lint_skip create mode 100644 tools/snpfreqplot/.lint_skip create mode 100644 tools/spaln/.lint_skip create mode 100644 tools/spotyping/.lint_skip create mode 100644 tools/stacks/.lint_skip create mode 100644 tools/stacks2/.lint_skip create mode 100644 tools/star_fusion/.lint_skip create mode 100644 tools/strelka/.lint_skip create mode 100644 tools/structure/.lint_skip create mode 100644 tools/structureharvester/.lint_skip create mode 100644 tools/swift/.lint_skip create mode 100644 tools/table_compute/.lint_skip create mode 100644 tools/tag_pileup_frequency/.lint_skip create mode 100644 tools/tasmanian_mismatch/.lint_skip create mode 100644 tools/tbl2gff3/.lint_skip create mode 100644 tools/telescope/.lint_skip create mode 100644 tools/tetyper/.lint_skip create mode 100644 tools/tn93/.lint_skip create mode 100644 tools/transdecoder/.lint_skip create mode 100644 tools/transit/.lint_skip create mode 100644 tools/trinotate/.lint_skip create mode 100644 tools/tsne/.lint_skip create mode 100644 tools/tximport/.lint_skip create mode 100644 tools/ucsc_blat/.lint_skip create mode 100644 tools/ucsc_tools/fasplit/.lint_skip create mode 100644 tools/ucsc_tools/twobittofa/.lint_skip create mode 100644 tools/umi_tools/.lint_skip create mode 100644 tools/varscan/.lint_skip create mode 100644 tools/vcf2maf/.lint_skip create mode 100644 tools/velvet/.lint_skip create mode 100644 tools/vg/.lint_skip create mode 100644 tools/vsearch/.lint_skip create mode 100644 tools/vsnp/.lint_skip create mode 100644 tools/winnowmap/.lint_skip create mode 100644 tools/xpath/.lint_skip diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index f2ecdfe79a3..95a09fa0a8c 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -75,7 +75,7 @@ jobs: echo 'Using ${{ steps.discover.outputs.chunk-count }} chunks (${{ steps.discover.outputs.chunk-list }})' lint: - name: Check for missing containers + name: Lint tool-list needs: setup if: ${{ needs.setup.outputs.repository-list != '' || needs.setup.outputs.tool-list != '' }} runs-on: ubuntu-latest @@ -101,9 +101,10 @@ jobs: id: lint with: mode: lint + fail-level: warn repository-list: ${{ needs.setup.outputs.repository-list }} tool-list: ${{ needs.setup.outputs.tool-list }} - additional-planemo-options: --biocontainers -s stdio,tests,output,inputs,help,general,command,citations,tool_xsd,xml_order,tool_urls,shed_metadata,urls,readme,shed_yaml,repository_dependencies,tool_dependencies_actions,tool_dependencies_sha256sum,tool_dependencies_xsd,expansion + additional-planemo-options: --biocontainers - uses: actions/upload-artifact@v4 if: ${{ failure() }} with: diff --git a/.github/workflows/pr.yaml b/.github/workflows/pr.yaml index eccab2f5c9b..87249ab8fcf 100644 --- a/.github/workflows/pr.yaml +++ b/.github/workflows/pr.yaml @@ -123,21 +123,12 @@ jobs: with: path: ~/.cache/pip key: pip_cache_py_${{ matrix.python-version }}_gxy_${{ needs.setup.outputs.galaxy-head-sha }} - - - name: Set fail level for pull request - if: ${{ github.event_name == 'pull_request' }} - run: - echo "FAIL_LEVEL=warn" >> "$GITHUB_ENV" - - name: Set fail level for merge - if: ${{ github.event_name != 'pull_request' }} - run: - echo "FAIL_LEVEL=error" >> "$GITHUB_ENV" - name: Planemo lint uses: galaxyproject/planemo-ci-action@v1 id: lint with: mode: lint - fail-level: ${{ env.FAIL_LEVEL }} + fail-level: warn repository-list: ${{ needs.setup.outputs.repository-list }} tool-list: ${{ needs.setup.outputs.tool-list }} - uses: actions/upload-artifact@v4 diff --git a/data_managers/data_manager_bowtie2_index_builder/.lint_skip b/data_managers/data_manager_bowtie2_index_builder/.lint_skip new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/data_managers/data_manager_bowtie2_index_builder/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/data_managers/data_manager_bowtie_index_builder/.lint_skip b/data_managers/data_manager_bowtie_index_builder/.lint_skip new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/data_managers/data_manager_bowtie_index_builder/.lint_skip @@ -0,0 +1 @@ +TestsMissing diff --git a/data_managers/data_manager_build_kma_index/.lint_skip b/data_managers/data_manager_build_kma_index/.lint_skip new file mode 100644 index 00000000000..7d044e96aea --- /dev/null +++ b/data_managers/data_manager_build_kma_index/.lint_skip @@ -0,0 +1 @@ +HelpEmpty diff --git a/data_managers/data_manager_build_kraken_database/.lint_skip b/data_managers/data_manager_build_kraken_database/.lint_skip new file mode 100644 index 00000000000..b394139e289 --- /dev/null +++ b/data_managers/data_manager_build_kraken_database/.lint_skip @@ -0,0 +1,2 @@ +HelpEmpty +TestsMissing diff --git a/data_managers/data_manager_bwa_mem_index_builder/.lint_skip b/data_managers/data_manager_bwa_mem_index_builder/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_bwa_mem_index_builder/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_fetch_gene_annotation/.lint_skip b/data_managers/data_manager_fetch_gene_annotation/.lint_skip new file mode 100644 index 00000000000..3e5615e7bb9 --- /dev/null +++ b/data_managers/data_manager_fetch_gene_annotation/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +HelpEmpty +TestsMissing diff --git a/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_fetch_index_maf/.lint_skip b/data_managers/data_manager_fetch_index_maf/.lint_skip new file mode 100644 index 00000000000..0518d2c178a --- /dev/null +++ b/data_managers/data_manager_fetch_index_maf/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +TestsMissing diff --git a/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip b/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_fetch_ncbi_taxonomy/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_gatk_picard_index_builder/.lint_skip b/data_managers/data_manager_gatk_picard_index_builder/.lint_skip new file mode 100644 index 00000000000..0518d2c178a --- /dev/null +++ b/data_managers/data_manager_gatk_picard_index_builder/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +TestsMissing diff --git a/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_genomic_super_signature_ravmodels/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_gtdbtk_database_installer/.lint_skip b/data_managers/data_manager_gtdbtk_database_installer/.lint_skip new file mode 100644 index 00000000000..7d044e96aea --- /dev/null +++ b/data_managers/data_manager_gtdbtk_database_installer/.lint_skip @@ -0,0 +1 @@ +HelpEmpty diff --git a/data_managers/data_manager_homer_preparsed/.lint_skip b/data_managers/data_manager_homer_preparsed/.lint_skip new file mode 100644 index 00000000000..a85f2705a91 --- /dev/null +++ b/data_managers/data_manager_homer_preparsed/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +HelpEmpty +XMLOrder diff --git a/data_managers/data_manager_kallisto_index_builder/.lint_skip b/data_managers/data_manager_kallisto_index_builder/.lint_skip new file mode 100644 index 00000000000..c779596e7cc --- /dev/null +++ b/data_managers/data_manager_kallisto_index_builder/.lint_skip @@ -0,0 +1,2 @@ +HelpInvalidRST +TestsMissing diff --git a/data_managers/data_manager_malt_index_builder/.lint_skip b/data_managers/data_manager_malt_index_builder/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_malt_index_builder/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_manual/.lint_skip b/data_managers/data_manager_manual/.lint_skip new file mode 100644 index 00000000000..e9fed198f57 --- /dev/null +++ b/data_managers/data_manager_manual/.lint_skip @@ -0,0 +1,3 @@ +CitationsMissing +InputsSelectDynamicOptions +XMLOrder diff --git a/data_managers/data_manager_mash_sketch_builder/.lint_skip b/data_managers/data_manager_mash_sketch_builder/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_mash_sketch_builder/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_mothur_toolsuite/.lint_skip b/data_managers/data_manager_mothur_toolsuite/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_mothur_toolsuite/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_packaged_annotation_data/.lint_skip b/data_managers/data_manager_packaged_annotation_data/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_packaged_annotation_data/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_pangolin_data/.lint_skip b/data_managers/data_manager_pangolin_data/.lint_skip new file mode 100644 index 00000000000..6a91ffad01c --- /dev/null +++ b/data_managers/data_manager_pangolin_data/.lint_skip @@ -0,0 +1,2 @@ +RequirementVersionMissing +XMLOrder diff --git a/data_managers/data_manager_picard_index_builder/.lint_skip b/data_managers/data_manager_picard_index_builder/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_picard_index_builder/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_qiime_database_downloader/.lint_skip b/data_managers/data_manager_qiime_database_downloader/.lint_skip new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/data_managers/data_manager_qiime_database_downloader/.lint_skip @@ -0,0 +1 @@ +TestsMissing diff --git a/data_managers/data_manager_salmon_index_builder/.lint_skip b/data_managers/data_manager_salmon_index_builder/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_salmon_index_builder/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_sam_fasta_index_builder/.lint_skip b/data_managers/data_manager_sam_fasta_index_builder/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_sam_fasta_index_builder/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_selection_background/.lint_skip b/data_managers/data_manager_selection_background/.lint_skip new file mode 100644 index 00000000000..d3a1493f388 --- /dev/null +++ b/data_managers/data_manager_selection_background/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +HelpEmpty diff --git a/data_managers/data_manager_semibin/.lint_skip b/data_managers/data_manager_semibin/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_semibin/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_snpeff/.lint_skip b/data_managers/data_manager_snpeff/.lint_skip new file mode 100644 index 00000000000..ac58e24884a --- /dev/null +++ b/data_managers/data_manager_snpeff/.lint_skip @@ -0,0 +1,2 @@ +InputsMissing +ToolVersionPEP404 diff --git a/data_managers/data_manager_star_index_builder/.lint_skip b/data_managers/data_manager_star_index_builder/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/data_managers/data_manager_star_index_builder/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/data_managers/data_manager_twobit_builder/.lint_skip b/data_managers/data_manager_twobit_builder/.lint_skip new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/data_managers/data_manager_twobit_builder/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/data_managers/data_manager_vsnp_dnaprints/.lint_skip b/data_managers/data_manager_vsnp_dnaprints/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_dnaprints/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/data_managers/data_manager_vsnp_excel/.lint_skip b/data_managers/data_manager_vsnp_excel/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_excel/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/data_managers/data_manager_vsnp_genbank/.lint_skip b/data_managers/data_manager_vsnp_genbank/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_genbank/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tool_collections/cufflinks/cuffdiff/.lint_skip b/tool_collections/cufflinks/cuffdiff/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tool_collections/cufflinks/cuffdiff/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tool_collections/cufflinks/cuffnorm/.lint_skip b/tool_collections/cufflinks/cuffnorm/.lint_skip new file mode 100644 index 00000000000..db401a876bb --- /dev/null +++ b/tool_collections/cufflinks/cuffnorm/.lint_skip @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +OutputsNameDuplicated diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip new file mode 100644 index 00000000000..f1a9e0e1123 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/.lint_skip @@ -0,0 +1 @@ +InputsSelectOptionsDeprecatedAttr diff --git a/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_combiner/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_filter/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_groomer/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip new file mode 100644 index 00000000000..5a3d475d5d1 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.lint_skip @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_stats/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip b/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastqtofasta/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/snpeff/.lint_skip b/tool_collections/snpeff/.lint_skip new file mode 100644 index 00000000000..a505b27b40f --- /dev/null +++ b/tool_collections/snpeff/.lint_skip @@ -0,0 +1,3 @@ +InputsDataOptionsFilterAttribFiltersType +InputsDataOptionsFiltersRef +TestsExpectNumOutputs diff --git a/tool_collections/snpsift/snpsift/.lint_skip b/tool_collections/snpsift/snpsift/.lint_skip new file mode 100644 index 00000000000..039bcb6e720 --- /dev/null +++ b/tool_collections/snpsift/snpsift/.lint_skip @@ -0,0 +1,2 @@ +TestsMissing +XMLOrder diff --git a/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip b/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tool_collections/snpsift/snpsift_dbnsfp/.lint_skip @@ -0,0 +1 @@ +TestsMissing diff --git a/tool_collections/snpsift/snpsift_genesets/.lint_skip b/tool_collections/snpsift/snpsift_genesets/.lint_skip new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tool_collections/snpsift/snpsift_genesets/.lint_skip @@ -0,0 +1 @@ +TestsMissing diff --git a/tool_collections/vcflib/vcffilter/.lint_skip b/tool_collections/vcflib/vcffilter/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tool_collections/vcflib/vcfsort/.lint_skip b/tool_collections/vcflib/vcfsort/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tool_collections/vcflib/vcfsort/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/abricate/.lint_skip b/tools/abricate/.lint_skip new file mode 100644 index 00000000000..0332c4d534d --- /dev/null +++ b/tools/abricate/.lint_skip @@ -0,0 +1,2 @@ +InputsMissing +XMLOrder diff --git a/tools/add_input_name_as_column/.lint_skip b/tools/add_input_name_as_column/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/add_input_name_as_column/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/allegro/.lint_skip b/tools/allegro/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/allegro/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/amplican/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/arriba/.lint_skip b/tools/arriba/.lint_skip new file mode 100644 index 00000000000..1d303e867c4 --- /dev/null +++ b/tools/arriba/.lint_skip @@ -0,0 +1 @@ +ValidatorExpression diff --git a/tools/art/.lint_skip b/tools/art/.lint_skip new file mode 100644 index 00000000000..de67bcbc665 --- /dev/null +++ b/tools/art/.lint_skip @@ -0,0 +1,4 @@ +ConditionalParamTypeBool +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/augustus/.lint_skip b/tools/augustus/.lint_skip new file mode 100644 index 00000000000..60dcaf138b5 --- /dev/null +++ b/tools/augustus/.lint_skip @@ -0,0 +1,5 @@ +InputsNameRedundantArgument +InputsSelectOptionDuplicateText +InputsSelectOptionDuplicateValue +TestsExpectNumOutputs +XMLOrder diff --git a/tools/b2btools/.lint_skip b/tools/b2btools/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/b2btools/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip new file mode 100644 index 00000000000..5c3b72bd205 --- /dev/null +++ b/tools/bamutil/.lint_skip @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +XMLOrder diff --git a/tools/barcode_splitter/.lint_skip b/tools/barcode_splitter/.lint_skip new file mode 100644 index 00000000000..db6945182f0 --- /dev/null +++ b/tools/barcode_splitter/.lint_skip @@ -0,0 +1,2 @@ +ConditionalWhenMissing +TestsExpectNumOutputs diff --git a/tools/baredsc/.lint_skip b/tools/baredsc/.lint_skip new file mode 100644 index 00000000000..c4bce2614c7 --- /dev/null +++ b/tools/baredsc/.lint_skip @@ -0,0 +1 @@ +EDAMTermsValid diff --git 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mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/megahit_contig2fastg/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/megan/.lint_skip b/tools/megan/.lint_skip new file mode 100644 index 00000000000..17796d16c43 --- /dev/null +++ b/tools/megan/.lint_skip @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +InputsNameRedundantArgument diff --git a/tools/meme/.lint_skip b/tools/meme/.lint_skip new file mode 100644 index 00000000000..d3e0aac05cd --- /dev/null +++ b/tools/meme/.lint_skip @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/merlin/.lint_skip b/tools/merlin/.lint_skip new file mode 100644 index 00000000000..281a52d416d --- /dev/null +++ b/tools/merlin/.lint_skip @@ -0,0 +1 @@ +OutputsLabelDuplicatedNoFilter diff --git a/tools/metaeuk/.lint_skip b/tools/metaeuk/.lint_skip new file mode 100644 index 00000000000..02cd7e2bd7e --- /dev/null +++ b/tools/metaeuk/.lint_skip @@ -0,0 +1,4 @@ +InputsNameRedundantArgument +OutputsLabelDuplicatedNoFilter +ToolVersionPEP404 +XMLOrder diff --git a/tools/metagenomeseq/.lint_skip b/tools/metagenomeseq/.lint_skip new file mode 100644 index 00000000000..005c9030cff --- /dev/null +++ b/tools/metagenomeseq/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +ToolVersionPEP404 diff --git a/tools/migmap/.lint_skip b/tools/migmap/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/migmap/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/minia/.lint_skip b/tools/minia/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/minia/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/mirnature/.lint_skip b/tools/mirnature/.lint_skip new file mode 100644 index 00000000000..561ac4b4543 --- /dev/null +++ b/tools/mirnature/.lint_skip @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/tools/mlst/.lint_skip b/tools/mlst/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/mlst/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/moabs/.lint_skip b/tools/moabs/.lint_skip new file mode 100644 index 00000000000..887ade8ade3 --- /dev/null +++ b/tools/moabs/.lint_skip @@ -0,0 +1 @@ +ConditionalWhenMissing diff --git a/tools/mothur/.lint_skip b/tools/mothur/.lint_skip new file mode 100644 index 00000000000..c538ac8fe2f --- /dev/null +++ b/tools/mothur/.lint_skip @@ -0,0 +1,5 @@ +HelpInvalidRST +OutputsLabelDuplicatedFilter +OutputsNameInvalidCheetah +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/msaboot/.lint_skip b/tools/msaboot/.lint_skip new file mode 100644 index 00000000000..c40bf0a2782 --- /dev/null +++ b/tools/msaboot/.lint_skip @@ -0,0 +1,2 @@ +InputsBoolDistinctValues +TestsExpectNumOutputs diff --git a/tools/multigps/.lint_skip b/tools/multigps/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/multigps/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml index d03a61523b4..e73e0a5d685 100644 --- a/tools/mummer4/macros.xml +++ b/tools/mummer4/macros.xml @@ -2,7 +2,7 @@ - mummer4 + mumer4 diff --git a/tools/mykrobe/.lint_skip b/tools/mykrobe/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/mykrobe/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/mzmine/.lint_skip b/tools/mzmine/.lint_skip new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tools/mzmine/.lint_skip @@ -0,0 +1 @@ +TestsMissing diff --git a/tools/naltorfs/.lint_skip b/tools/naltorfs/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/naltorfs/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/nanocompore/.lint_skip b/tools/nanocompore/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/nanocompore/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ncbi_acc_download/.lint_skip b/tools/ncbi_acc_download/.lint_skip new file mode 100644 index 00000000000..8300ec2e860 --- /dev/null +++ b/tools/ncbi_acc_download/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputs diff --git a/tools/ncbi_entrez_eutils/.lint_skip b/tools/ncbi_entrez_eutils/.lint_skip new file mode 100644 index 00000000000..8fac1952a0d --- /dev/null +++ b/tools/ncbi_entrez_eutils/.lint_skip @@ -0,0 +1,2 @@ +InputsNameDuplicate +TestsExpectNumOutputs diff --git a/tools/necat/.lint_skip b/tools/necat/.lint_skip new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/necat/.lint_skip @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/newick_utils/.lint_skip b/tools/newick_utils/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/newick_utils/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ngmlr/.lint_skip b/tools/ngmlr/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/ngmlr/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ngsutils/.lint_skip b/tools/ngsutils/.lint_skip new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/tools/ngsutils/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/tools/ococo/.lint_skip b/tools/ococo/.lint_skip new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/ococo/.lint_skip @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/odgi/.lint_skip b/tools/odgi/.lint_skip new file mode 100644 index 00000000000..8300ec2e860 --- /dev/null +++ b/tools/odgi/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputs diff --git a/tools/packaged_annotation_loader/.lint_skip b/tools/packaged_annotation_loader/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/packaged_annotation_loader/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/pathview/.lint_skip b/tools/pathview/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/pathview/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/pbgcpp/.lint_skip b/tools/pbgcpp/.lint_skip new file mode 100644 index 00000000000..9c757f1de60 --- /dev/null +++ b/tools/pbgcpp/.lint_skip @@ -0,0 +1,2 @@ +CitationsMissing +TestsExpectNumOutputs diff --git a/tools/pe_histogram/.lint_skip b/tools/pe_histogram/.lint_skip new file mode 100644 index 00000000000..281a52d416d --- /dev/null +++ b/tools/pe_histogram/.lint_skip @@ -0,0 +1 @@ +OutputsLabelDuplicatedNoFilter diff --git a/tools/picard/.lint_skip b/tools/picard/.lint_skip new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/picard/.lint_skip @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/picrust2/.lint_skip b/tools/picrust2/.lint_skip new file mode 100644 index 00000000000..208f465e2bc --- /dev/null +++ b/tools/picrust2/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputsFailing diff --git a/tools/pilon/.lint_skip b/tools/pilon/.lint_skip new file mode 100644 index 00000000000..eb2cdb1921c --- /dev/null +++ b/tools/pilon/.lint_skip @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs diff --git a/tools/pizzly/.lint_skip b/tools/pizzly/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/pizzly/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/plink/.lint_skip b/tools/plink/.lint_skip new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/plink/.lint_skip @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/porechop/.lint_skip b/tools/porechop/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/porechop/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/poretools/.lint_skip b/tools/poretools/.lint_skip new file mode 100644 index 00000000000..37306aaf5f8 --- /dev/null +++ b/tools/poretools/.lint_skip @@ -0,0 +1,7 @@ +InputsNameDuplicate +InputsNameRedundantArgument +InputsSelectOptionDuplicateText +InputsSelectOptionDuplicateValue +TestsParamInInputs +ToolVersionPEP404 +XMLOrder diff --git a/tools/presto/.lint_skip b/tools/presto/.lint_skip new file mode 100644 index 00000000000..88c3f1f4ea1 --- /dev/null +++ b/tools/presto/.lint_skip @@ -0,0 +1,4 @@ +OutputsLabelDuplicatedFilter +OutputsLabelDuplicatedNoFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/prinseq/.lint_skip b/tools/prinseq/.lint_skip new file mode 100644 index 00000000000..5c3b72bd205 --- /dev/null +++ b/tools/prinseq/.lint_skip @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +XMLOrder diff --git a/tools/progressivemauve/.lint_skip b/tools/progressivemauve/.lint_skip new file mode 100644 index 00000000000..f885163c07d --- /dev/null +++ b/tools/progressivemauve/.lint_skip @@ -0,0 +1,3 @@ +CitationsNoValid +HelpInvalidRST +ToolVersionPEP404 diff --git a/tools/prokka/.lint_skip b/tools/prokka/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/prokka/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/pureclip/.lint_skip b/tools/pureclip/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/pureclip/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/quickmerge/.lint_skip b/tools/quickmerge/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/quickmerge/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/raceid/.lint_skip b/tools/raceid/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/raceid/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rapidnj/.lint_skip b/tools/rapidnj/.lint_skip new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/rapidnj/.lint_skip @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/rcorrector/.lint_skip b/tools/rcorrector/.lint_skip new file mode 100644 index 00000000000..eb2cdb1921c --- /dev/null +++ b/tools/rcorrector/.lint_skip @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs diff --git a/tools/repeatmasker/.lint_skip b/tools/repeatmasker/.lint_skip new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/repeatmasker/.lint_skip @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/repmatch_gff3/.lint_skip b/tools/repmatch_gff3/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/repmatch_gff3/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/ribowaltz/.lint_skip b/tools/ribowaltz/.lint_skip new file mode 100644 index 00000000000..c4bce2614c7 --- /dev/null +++ b/tools/ribowaltz/.lint_skip @@ -0,0 +1 @@ +EDAMTermsValid diff --git a/tools/roary/.lint_skip b/tools/roary/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/roary/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rp2biosensor/.lint_skip b/tools/rp2biosensor/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/rp2biosensor/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rptools/.lint_skip b/tools/rptools/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/rptools/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/rrparser/.lint_skip b/tools/rrparser/.lint_skip new file mode 100644 index 00000000000..887ade8ade3 --- /dev/null +++ b/tools/rrparser/.lint_skip @@ -0,0 +1 @@ +ConditionalWhenMissing diff --git a/tools/ruvseq/.lint_skip b/tools/ruvseq/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/ruvseq/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/salsa2/.lint_skip b/tools/salsa2/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/salsa2/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/samblaster/.lint_skip b/tools/samblaster/.lint_skip new file mode 100644 index 00000000000..44e038a095b --- /dev/null +++ b/tools/samblaster/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/sbml2sbol/.lint_skip b/tools/sbml2sbol/.lint_skip new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/sbml2sbol/.lint_skip @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/scater/.lint_skip b/tools/scater/.lint_skip new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/scater/.lint_skip @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/scpipe/.lint_skip b/tools/scpipe/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/scpipe/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/seqcomplexity/.lint_skip b/tools/seqcomplexity/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/seqcomplexity/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/seqwish/.lint_skip b/tools/seqwish/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/seqwish/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/shorah/.lint_skip b/tools/shorah/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/shorah/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/sickle/.lint_skip b/tools/sickle/.lint_skip new file mode 100644 index 00000000000..561ac4b4543 --- /dev/null +++ b/tools/sickle/.lint_skip @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/tools/simtext/.lint_skip b/tools/simtext/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/simtext/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/sina/.lint_skip b/tools/sina/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/sina/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/slamdunk/.lint_skip b/tools/slamdunk/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/slamdunk/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/snap/.lint_skip b/tools/snap/.lint_skip new file mode 100644 index 00000000000..aff5d391aff --- /dev/null +++ b/tools/snap/.lint_skip @@ -0,0 +1,3 @@ +CitationsNoValid +ToolVersionPEP404 +XMLOrder diff --git a/tools/sniffles/.lint_skip b/tools/sniffles/.lint_skip new file mode 100644 index 00000000000..066d952b239 --- /dev/null +++ b/tools/sniffles/.lint_skip @@ -0,0 +1,2 @@ +TestsParamInInputs +XMLOrder diff --git a/tools/snippy/.lint_skip b/tools/snippy/.lint_skip new file mode 100644 index 00000000000..e6389d1e57b --- /dev/null +++ b/tools/snippy/.lint_skip @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs +XMLOrder diff --git a/tools/snp-dists/.lint_skip b/tools/snp-dists/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/snp-dists/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/snpeff-covid19/.lint_skip b/tools/snpeff-covid19/.lint_skip new file mode 100644 index 00000000000..38682cfa50a --- /dev/null +++ b/tools/snpeff-covid19/.lint_skip @@ -0,0 +1,3 @@ +TestsExpectNumOutputs +ToolVersionPEP404 +XMLOrder diff --git a/tools/snpfreqplot/.lint_skip b/tools/snpfreqplot/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/snpfreqplot/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/spaln/.lint_skip b/tools/spaln/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/spaln/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/spotyping/.lint_skip b/tools/spotyping/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/spotyping/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/stacks/.lint_skip b/tools/stacks/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/stacks/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/stacks2/.lint_skip b/tools/stacks2/.lint_skip new file mode 100644 index 00000000000..3f36fbca6c2 --- /dev/null +++ b/tools/stacks2/.lint_skip @@ -0,0 +1,3 @@ +CommandTODO +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter diff --git a/tools/star_fusion/.lint_skip b/tools/star_fusion/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/star_fusion/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/strelka/.lint_skip b/tools/strelka/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/strelka/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/structure/.lint_skip b/tools/structure/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/structure/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/structureharvester/.lint_skip b/tools/structureharvester/.lint_skip new file mode 100644 index 00000000000..4d97c7e23e6 --- /dev/null +++ b/tools/structureharvester/.lint_skip @@ -0,0 +1,2 @@ +InputsNameDuplicateOutput +TestsExpectNumOutputs diff --git a/tools/swift/.lint_skip b/tools/swift/.lint_skip new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/swift/.lint_skip @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/table_compute/.lint_skip b/tools/table_compute/.lint_skip new file mode 100644 index 00000000000..b5212db9362 --- /dev/null +++ b/tools/table_compute/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputsFailing diff --git a/tools/tag_pileup_frequency/.lint_skip b/tools/tag_pileup_frequency/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tag_pileup_frequency/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tasmanian_mismatch/.lint_skip b/tools/tasmanian_mismatch/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tasmanian_mismatch/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tbl2gff3/.lint_skip b/tools/tbl2gff3/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/tbl2gff3/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/telescope/.lint_skip b/tools/telescope/.lint_skip new file mode 100644 index 00000000000..5a3d475d5d1 --- /dev/null +++ b/tools/telescope/.lint_skip @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/tetyper/.lint_skip b/tools/tetyper/.lint_skip new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tetyper/.lint_skip @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tn93/.lint_skip b/tools/tn93/.lint_skip new file mode 100644 index 00000000000..232ad9b2230 --- /dev/null +++ b/tools/tn93/.lint_skip @@ -0,0 +1,2 @@ +HelpInvalidRST +OutputsLabelDuplicatedFilter diff --git a/tools/transdecoder/.lint_skip b/tools/transdecoder/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/transdecoder/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/transit/.lint_skip b/tools/transit/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/transit/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/trinotate/.lint_skip b/tools/trinotate/.lint_skip new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/trinotate/.lint_skip @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/tsne/.lint_skip b/tools/tsne/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/tsne/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/tximport/.lint_skip b/tools/tximport/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/tximport/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ucsc_blat/.lint_skip b/tools/ucsc_blat/.lint_skip new file mode 100644 index 00000000000..a1cf37844af --- /dev/null +++ b/tools/ucsc_blat/.lint_skip @@ -0,0 +1 @@ +TestsOutputCompareAttrib diff --git a/tools/ucsc_tools/fasplit/.lint_skip b/tools/ucsc_tools/fasplit/.lint_skip new file mode 100644 index 00000000000..af4cf5ec3d4 --- /dev/null +++ b/tools/ucsc_tools/fasplit/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +XMLOrder diff --git a/tools/ucsc_tools/twobittofa/.lint_skip b/tools/ucsc_tools/twobittofa/.lint_skip new file mode 100644 index 00000000000..af4cf5ec3d4 --- /dev/null +++ b/tools/ucsc_tools/twobittofa/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +XMLOrder diff --git a/tools/umi_tools/.lint_skip b/tools/umi_tools/.lint_skip new file mode 100644 index 00000000000..dc4adbb445e --- /dev/null +++ b/tools/umi_tools/.lint_skip @@ -0,0 +1,6 @@ +CommandTODO +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +TestsParamInInputs +XMLOrder diff --git a/tools/varscan/.lint_skip b/tools/varscan/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/varscan/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/vcf2maf/.lint_skip b/tools/vcf2maf/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/vcf2maf/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/velvet/.lint_skip b/tools/velvet/.lint_skip new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/velvet/.lint_skip @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/vg/.lint_skip b/tools/vg/.lint_skip new file mode 100644 index 00000000000..02e7f1dcf79 --- /dev/null +++ b/tools/vg/.lint_skip @@ -0,0 +1,2 @@ +CitationsNoValid +HelpInvalidRST diff --git a/tools/vsearch/.lint_skip b/tools/vsearch/.lint_skip new file mode 100644 index 00000000000..de4e58e9ed1 --- /dev/null +++ b/tools/vsearch/.lint_skip @@ -0,0 +1,3 @@ +InputsSelectOptionDuplicateText +TestsExpectNumOutputs +XMLOrder diff --git a/tools/vsnp/.lint_skip b/tools/vsnp/.lint_skip new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/vsnp/.lint_skip @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/winnowmap/.lint_skip b/tools/winnowmap/.lint_skip new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/winnowmap/.lint_skip @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/xpath/.lint_skip b/tools/xpath/.lint_skip new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/xpath/.lint_skip @@ -0,0 +1 @@ +CitationsNoValid From 86a73647ee5b82fd650768452b23177722c64d19 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Mon, 29 Jul 2024 12:33:44 +0200 Subject: [PATCH 02/15] undo changes to tool --- tools/mummer4/.lint_skip | 1 + tools/mummer4/macros.xml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) create mode 100644 tools/mummer4/.lint_skip diff --git a/tools/mummer4/.lint_skip b/tools/mummer4/.lint_skip new file mode 100644 index 00000000000..93b5ffc68a8 --- /dev/null +++ b/tools/mummer4/.lint_skip @@ -0,0 +1 @@ +BioToolsValid diff --git a/tools/mummer4/macros.xml b/tools/mummer4/macros.xml index e73e0a5d685..d03a61523b4 100644 --- a/tools/mummer4/macros.xml +++ b/tools/mummer4/macros.xml @@ -2,7 +2,7 @@ - mumer4 + mummer4 From 0035534268390396054e0b6fc1a45022ba05671c Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 16:47:14 +0200 Subject: [PATCH 03/15] fix linting errors in abricate --- tools/abricate/.lint_skip | 2 -- tools/abricate/abricate.xml | 34 +++++++++-------------------- tools/abricate/abricate_list.xml | 17 +++++---------- tools/abricate/abricate_summary.xml | 18 +++++---------- tools/abricate/macros.xml | 19 ++++++---------- 5 files changed, 29 insertions(+), 61 deletions(-) delete mode 100644 tools/abricate/.lint_skip diff --git a/tools/abricate/.lint_skip b/tools/abricate/.lint_skip deleted file mode 100644 index 0332c4d534d..00000000000 --- a/tools/abricate/.lint_skip +++ /dev/null @@ -1,2 +0,0 @@ -InputsMissing -XMLOrder diff --git a/tools/abricate/abricate.xml b/tools/abricate/abricate.xml index e7d0dbdf3a5..b8c1c7d1a1f 100644 --- a/tools/abricate/abricate.xml +++ b/tools/abricate/abricate.xml @@ -5,11 +5,10 @@ macros.xml - - - - - + + + + '$report' ]]> - - +
@@ -42,72 +40,61 @@ - - - + + +
- - + - - + - - - - - - - - - - diff --git a/tools/abricate/abricate_list.xml b/tools/abricate/abricate_list.xml index d82cc81c48e..f46514675af 100644 --- a/tools/abricate/abricate_list.xml +++ b/tools/abricate/abricate_list.xml @@ -5,33 +5,28 @@ macros.xml - - - - - + + + + '$report' ]]> - + - - - + - - diff --git a/tools/abricate/abricate_summary.xml b/tools/abricate/abricate_summary.xml index ef236cca5a0..ed6cdf8f62f 100644 --- a/tools/abricate/abricate_summary.xml +++ b/tools/abricate/abricate_summary.xml @@ -5,11 +5,10 @@ macros.xml - - - - - + + + + '$summary' ]]> - - + - - - + - - diff --git a/tools/abricate/macros.xml b/tools/abricate/macros.xml index 41230e4c1f9..864685afba3 100644 --- a/tools/abricate/macros.xml +++ b/tools/abricate/macros.xml @@ -2,17 +2,14 @@ abricate - + - - 1.0.1 20.01 - topic_0622 @@ -22,16 +19,14 @@ operation_3482 - - - ABRicate - + + ABRicate + - - - + + @UNPUBLISHED{Seemann2016, author = {Seemann, Torsten}, title = {ABRicate: mass screening of contigs for antiobiotic resistance genes}, @@ -39,6 +34,6 @@ url = {https://github.com/tseemann/abricate}, } - + From 406d8c2ddff625866f01047a56791912b1262377 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 16:50:13 +0200 Subject: [PATCH 04/15] fix amplican --- tools/amplican/.lint_skip | 1 - tools/amplican/amplican.xml | 139 +++++++++++++++++------------------- 2 files changed, 67 insertions(+), 73 deletions(-) delete mode 100644 tools/amplican/.lint_skip diff --git a/tools/amplican/.lint_skip b/tools/amplican/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/amplican/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/amplican/amplican.xml b/tools/amplican/amplican.xml index cb4a8938953..e2b731b0f97 100644 --- a/tools/amplican/amplican.xml +++ b/tools/amplican/amplican.xml @@ -1,11 +1,11 @@ - + analysis tool for genome editing macros.xml - - + - - + - + - +
- - + +
- - - - + + + +
- + @@ -114,10 +109,10 @@ - - - - + + + +
@@ -125,19 +120,19 @@ - - - - - - - - - - + + + + + + + + + +
- + "config_summary" in output_options["outputs"] @@ -176,8 +171,8 @@ - - + +
@@ -200,66 +195,66 @@ -
+
- + - + - + - + - + - + - + - + - + - + - - + +
@@ -287,61 +282,61 @@
- + - + - + - + - + - + - + - + - + - + - + - + - + - + - - + +
@@ -371,31 +366,31 @@
- + - + - - + +
- + - + @@ -434,5 +429,5 @@ Columns of the config file: If you have only forward primers leave column Reverse_Primer empty, leave empty also the Reverse_Reads column. You can still use amplican like normal. ]]> - + From c8fee7eceb893d62f3373d75f83170a8731d4763 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 16:56:31 +0200 Subject: [PATCH 05/15] fix lint in bamutils --- tools/bamutil/.lint_skip | 3 +-- tools/bamutil/clip_overlap.xml | 2 +- tools/bamutil/diff.xml | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/bamutil/.lint_skip b/tools/bamutil/.lint_skip index 5c3b72bd205..799954db976 100644 --- a/tools/bamutil/.lint_skip +++ b/tools/bamutil/.lint_skip @@ -1,2 +1 @@ -OutputsLabelDuplicatedFilter -XMLOrder +OutputsLabelDuplicatedFilter \ No newline at end of file diff --git a/tools/bamutil/clip_overlap.xml b/tools/bamutil/clip_overlap.xml index e8c90b17ac7..87f9a69b81c 100644 --- a/tools/bamutil/clip_overlap.xml +++ b/tools/bamutil/clip_overlap.xml @@ -3,8 +3,8 @@ macros.xml - + macros.xml - + Date: Sun, 25 Aug 2024 16:58:30 +0200 Subject: [PATCH 06/15] fix barrnap linting --- tools/barrnap/.lint_skip | 1 - tools/barrnap/barrnap.xml | 8 ++++---- 2 files changed, 4 insertions(+), 5 deletions(-) delete mode 100644 tools/barrnap/.lint_skip diff --git a/tools/barrnap/.lint_skip b/tools/barrnap/.lint_skip deleted file mode 100644 index cc60dd28c7b..00000000000 --- a/tools/barrnap/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -TestsExpectNumOutputs diff --git a/tools/barrnap/barrnap.xml b/tools/barrnap/barrnap.xml index a1edc9f00ac..88a464dddc6 100644 --- a/tools/barrnap/barrnap.xml +++ b/tools/barrnap/barrnap.xml @@ -52,24 +52,24 @@ - + - + - + - + From 692e18720cd1a4403e2dc7bce5f1e0ec4ae10c09 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:00:10 +0200 Subject: [PATCH 07/15] fix bioperl linting --- tools/bioperl/.lint_skip | 1 - tools/bioperl/bp_genbank2gff3.xml | 2 +- 2 files changed, 1 insertion(+), 2 deletions(-) delete mode 100644 tools/bioperl/.lint_skip diff --git a/tools/bioperl/.lint_skip b/tools/bioperl/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/bioperl/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/bioperl/bp_genbank2gff3.xml b/tools/bioperl/bp_genbank2gff3.xml index e3ffe5c75a9..cc09865ea83 100644 --- a/tools/bioperl/bp_genbank2gff3.xml +++ b/tools/bioperl/bp_genbank2gff3.xml @@ -1,9 +1,9 @@ converter - macros.xml + Date: Sun, 25 Aug 2024 17:01:34 +0200 Subject: [PATCH 08/15] fix cdhit --- tools/cdhit/.lint_skip | 1 - tools/cdhit/cd_hit.xml | 69 ++++++++++++++++++++---------------------- 2 files changed, 33 insertions(+), 37 deletions(-) delete mode 100644 tools/cdhit/.lint_skip diff --git a/tools/cdhit/.lint_skip b/tools/cdhit/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/cdhit/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/cdhit/cd_hit.xml b/tools/cdhit/cd_hit.xml index f881b6e353d..704504c6e98 100644 --- a/tools/cdhit/cd_hit.xml +++ b/tools/cdhit/cd_hit.xml @@ -3,8 +3,8 @@ macros.xml - + @@ -117,9 +117,9 @@ $advanced.sort_fasta - + - + @@ -131,8 +131,8 @@ $advanced.sort_fasta
- - + +
@@ -141,10 +141,9 @@ $advanced.sort_fasta - - + + - @@ -156,42 +155,40 @@ $advanced.sort_fasta - - - + - + - - + + - + - + - + - - + + - +
- - + +
@@ -203,12 +200,12 @@ $advanced.sort_fasta - + - + - + @@ -218,13 +215,13 @@ $advanced.sort_fasta - + - - + + - + @@ -234,12 +231,12 @@ $advanced.sort_fasta - + - + - + @@ -252,12 +249,12 @@ $advanced.sort_fasta - + - + - + @@ -318,5 +315,5 @@ For cd-hit-2d and cd-hit-est-2d: 2. The second output is a text file that lists similar sequences between db1 & db2 ]]> - + From 714fb9646fc7fb4a2123ef9401ad550d2ef68bc9 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:02:54 +0200 Subject: [PATCH 09/15] fix circexplorer2 linting --- tools/circexplorer2/.lint_skip | 1 - tools/circexplorer2/circexplorer2.xml | 311 ++++++++++++-------------- tools/circexplorer2/macros.xml | 16 +- 3 files changed, 144 insertions(+), 184 deletions(-) delete mode 100644 tools/circexplorer2/.lint_skip diff --git a/tools/circexplorer2/.lint_skip b/tools/circexplorer2/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/circexplorer2/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/circexplorer2/circexplorer2.xml b/tools/circexplorer2/circexplorer2.xml index 8aa7599035e..ed8604328cc 100644 --- a/tools/circexplorer2/circexplorer2.xml +++ b/tools/circexplorer2/circexplorer2.xml @@ -3,8 +3,8 @@ macros.xml - - + + - + @@ -90,56 +85,42 @@ - + - - - - - + + + + + - + - - + + - + - + - + - + - + @@ -148,52 +129,36 @@ - - + + - + - - + + - - - + + + - + - - + + @@ -256,117 +221,117 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + - - - - - - - - - - - + + + + + + + + + + + + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_, including installation instructions and tutorial. ]]> - + diff --git a/tools/circexplorer2/macros.xml b/tools/circexplorer2/macros.xml index 4f739c5a984..88dbf9376fa 100644 --- a/tools/circexplorer2/macros.xml +++ b/tools/circexplorer2/macros.xml @@ -15,28 +15,24 @@ - + - + - + - + - + 10.1101/gr.202895.115 - \ No newline at end of file + From 42c65c41e13395f6716afc501ce59b0b2de35837 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:06:56 +0200 Subject: [PATCH 10/15] fix crossmap linting --- tools/crossmap/.lint_skip | 1 - tools/crossmap/crossmap_bam.xml | 17 +++------- tools/crossmap/crossmap_bed.xml | 53 ++++++++++++------------------ tools/crossmap/crossmap_bigwig.xml | 15 +++------ tools/crossmap/crossmap_gff.xml | 17 +++------- tools/crossmap/crossmap_region.xml | 6 ++-- tools/crossmap/crossmap_vcf.xml | 17 +++------- tools/crossmap/crossmap_wig.xml | 21 ++++-------- tools/crossmap/macros.xml | 1 - 9 files changed, 47 insertions(+), 101 deletions(-) delete mode 100644 tools/crossmap/.lint_skip diff --git a/tools/crossmap/.lint_skip b/tools/crossmap/.lint_skip deleted file mode 100644 index cc60dd28c7b..00000000000 --- a/tools/crossmap/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -TestsExpectNumOutputs diff --git a/tools/crossmap/crossmap_bam.xml b/tools/crossmap/crossmap_bam.xml index 1f2394d0b54..f376e3f99ac 100644 --- a/tools/crossmap/crossmap_bam.xml +++ b/tools/crossmap/crossmap_bam.xml @@ -23,33 +23,27 @@ output ]]> - - - + - - + - - + - - + - + - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_bed.xml b/tools/crossmap/crossmap_bed.xml index 89c0f8f365b..ca32867a028 100644 --- a/tools/crossmap/crossmap_bed.xml +++ b/tools/crossmap/crossmap_bed.xml @@ -6,8 +6,7 @@ - - + + - - + - + + - - + - - + + - - - + + - + + - - - + + - - + + - - + @@ -141,7 +131,6 @@ Notes: 7. If input region cannot be consecutively mapped target assembly, it will be split. 8. \*.unmap file contains regions that cannot be unambiguously converted. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_bigwig.xml b/tools/crossmap/crossmap_bigwig.xml index c289408f457..713cb2de92c 100644 --- a/tools/crossmap/crossmap_bigwig.xml +++ b/tools/crossmap/crossmap_bigwig.xml @@ -6,36 +6,30 @@ - - - - + - - + - - - + + - @@ -53,7 +47,6 @@ wigToBigWig tool. We export files in bedGraph because it is usually much smaller than file in wiggle format, and more importantly, CrossMap internally transforms wiggle into bedGraph to increase running speed. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_gff.xml b/tools/crossmap/crossmap_gff.xml index 97a10a0a662..a8b0aab20bb 100644 --- a/tools/crossmap/crossmap_gff.xml +++ b/tools/crossmap/crossmap_gff.xml @@ -6,7 +6,6 @@ - - - - - + - - + - - @@ -45,14 +38,13 @@ output - - + + - @@ -75,7 +67,6 @@ Notes: the same gene were converted into the same gene. - If user want to liftover gene annotation files, use BED12 format. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_region.xml b/tools/crossmap/crossmap_region.xml index 32cc3021e82..473bcd669b2 100644 --- a/tools/crossmap/crossmap_region.xml +++ b/tools/crossmap/crossmap_region.xml @@ -15,9 +15,8 @@ CrossMap.py region --ratio $ratio ]]> - - + + @@ -78,7 +77,6 @@ Notes: 7. If input region cannot be consecutively mapped target assembly, it will be split. 8. \*.unmap file contains regions that cannot be unambiguously converted. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_vcf.xml b/tools/crossmap/crossmap_vcf.xml index 57d8062a5f2..cd97308ccd9 100644 --- a/tools/crossmap/crossmap_vcf.xml +++ b/tools/crossmap/crossmap_vcf.xml @@ -6,7 +6,6 @@ - - @@ -45,25 +43,20 @@ output - - + - - - + - - - + + - @@ -71,7 +64,6 @@ output - @@ -108,7 +100,6 @@ Notes: - In the output VCF file, whether the chromosome IDs contain “chr” or not depends on the format of the input VCF file. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/crossmap_wig.xml b/tools/crossmap/crossmap_wig.xml index e61c6832e07..77155032a53 100644 --- a/tools/crossmap/crossmap_wig.xml +++ b/tools/crossmap/crossmap_wig.xml @@ -12,33 +12,27 @@ CrossMap.py wig '${input}' output ]]> - - - + - - - + + - - + - - - - + + + - @@ -57,7 +51,6 @@ wigToBigWig tool. We export files in bedGraph because it is usually much smaller than file in wiggle format, and more importantly, CrossMap internally transforms wiggle into bedGraph to increase running speed. ]]> - 10.1093/bioinformatics/btt730 diff --git a/tools/crossmap/macros.xml b/tools/crossmap/macros.xml index 0e59dfd4eb1..8c498fc48c3 100644 --- a/tools/crossmap/macros.xml +++ b/tools/crossmap/macros.xml @@ -1,4 +1,3 @@ - From 83d1ec6b9e35707b106aac660383c89e0a37bc32 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:09:39 +0200 Subject: [PATCH 11/15] fix delly linting --- tools/delly/.lint_skip | 1 - tools/delly/call.xml | 2 +- tools/delly/classify.xml | 1 + tools/delly/cnv.xml | 2 +- tools/delly/filter.xml | 2 +- tools/delly/lr.xml | 13 ++++++------- tools/delly/macros.xml | 12 ++---------- tools/delly/merge.xml | 9 ++++----- 8 files changed, 16 insertions(+), 26 deletions(-) delete mode 100644 tools/delly/.lint_skip diff --git a/tools/delly/.lint_skip b/tools/delly/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/delly/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/delly/call.xml b/tools/delly/call.xml index 3c6729f5815..c441b8fdb95 100644 --- a/tools/delly/call.xml +++ b/tools/delly/call.xml @@ -1,10 +1,10 @@ and genotype structural variants - macros.xml + macros.xml + discover and genotype copy-number variants - macros.xml + somatic or germline structural variants - macros.xml + optimized calling and genotyping of structural variants - macros.xml + - + @@ -134,7 +133,7 @@ delly lr - +
@@ -211,7 +210,7 @@ delly lr - + @@ -228,7 +227,7 @@ delly lr - + @@ -303,4 +302,4 @@ The output is available in BCF and VCF format. Additionally an output file for S @REFERENCES@ ]]> - \ No newline at end of file + diff --git a/tools/delly/macros.xml b/tools/delly/macros.xml index ca73754e361..e4aab2fb6a2 100644 --- a/tools/delly/macros.xml +++ b/tools/delly/macros.xml @@ -1,4 +1,3 @@ - 0.9.1 1 @@ -11,7 +10,7 @@ &1 | grep 'Delly version' | cut -f 3 -d ' ']]> - + 10.1093/bioinformatics/bts378 @@ -22,7 +21,6 @@ - 'result.vcf' || echo 'No results.' #end if ]]> - - @@ -71,7 +67,7 @@ ln -s '$generic.genome' genome.fa && - + @@ -113,9 +109,7 @@ ln -s '$generic.genome' genome.fa && - - 'bcf' in oo['out'] @@ -136,9 +130,7 @@ ln -s '$generic.genome' genome.fa && 'log' in oo['out'] - - structural variants across/within BCF/VCF file(s) - macros.xml + - + @@ -126,7 +125,7 @@ $generic.pass - + @@ -145,7 +144,7 @@ $generic.pass - + From ff16af6bc248259ae63a55a4606ac02b03accde4 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:12:06 +0200 Subject: [PATCH 12/15] fix dropletutils --- tools/dropletutils/.lint_skip | 1 - tools/dropletutils/dropletutils.xml | 204 ++++++++++++++-------------- 2 files changed, 103 insertions(+), 102 deletions(-) delete mode 100644 tools/dropletutils/.lint_skip diff --git a/tools/dropletutils/.lint_skip b/tools/dropletutils/.lint_skip deleted file mode 100644 index a68d017209e..00000000000 --- a/tools/dropletutils/.lint_skip +++ /dev/null @@ -1 +0,0 @@ -XMLOrder diff --git a/tools/dropletutils/dropletutils.xml b/tools/dropletutils/dropletutils.xml index 7e10bd31ace..9bee524f9f3 100644 --- a/tools/dropletutils/dropletutils.xml +++ b/tools/dropletutils/dropletutils.xml @@ -1,10 +1,19 @@ - - + Utilities for handling droplet-based single-cell RNA-seq data - - dropletutils - dropletutils - + + 1.10.0 + 2 + tenx.input + tenx.output + + + + + + + + + topic_0203 topic_3168 @@ -15,23 +24,13 @@ operation_1812 operation_3200 - - 1.10.0 - 2 - tenx.input - tenx.output - - - - - - - - - + + dropletutils + dropletutils + bioconductor-dropletutils - bioconductor-scater + bioconductor-scater r-base r-matrix fonts-conda-ecosystem @@ -40,7 +39,7 @@ Rscript -e 'packageVersion("DropletUtils")' | grep -oP '\d\.\d\.\d' ]]> - - + ## defaults empty_fdr_threshold = 0.01 eparams = formals(emptyDrops) @@ -113,8 +112,8 @@ seed.val=as.integer('$seed') - - + + @@ -126,33 +125,33 @@ seed.val=as.integer('$seed') - + - + - + - - - + + + - - + + - - + + @@ -160,7 +159,7 @@ seed.val=as.integer('$seed') - + @@ -169,13 +168,13 @@ seed.val=as.integer('$seed') operation['use']=='filter' and operation['outformat'] == 'h5' - + operation['use']=='filter' and operation['outformat'] == 'directory' - + operation['use']=='filter' and operation['outformat'] == 'directory' - + operation['use']=='filter' and operation['outformat'] == 'directory' @@ -189,119 +188,122 @@ seed.val=as.integer('$seed') - + - - + + + - + - + - - + + + - + - - - - + + + + - + - - + + - + - + - - + + - - - + + + - - + + - - - - + + + + - + - - - + + + - - + + - - - + + + - - + + - - - - + + + + - + - - - + + + - - + + - - - - + + + + - - + + + - - - + + + - + - - - + + + From 546a0ebe8726aea95b0ec3be3834ac1eae993ffe Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:29:54 +0200 Subject: [PATCH 13/15] reset autoformat --- tools/delly/lr.xml | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/tools/delly/lr.xml b/tools/delly/lr.xml index d76edb3ee05..a44bc52cc7c 100644 --- a/tools/delly/lr.xml +++ b/tools/delly/lr.xml @@ -1,3 +1,4 @@ + optimized calling and genotyping of structural variants @@ -104,7 +105,7 @@ delly lr - + @@ -133,7 +134,7 @@ delly lr - +
@@ -210,7 +211,7 @@ delly lr - + @@ -227,7 +228,7 @@ delly lr - + From 7950412b36239e09cd74a9d6e262952bdbd9b753 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sun, 25 Aug 2024 17:30:56 +0200 Subject: [PATCH 14/15] reset autoformat --- tools/delly/merge.xml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/tools/delly/merge.xml b/tools/delly/merge.xml index 4f53eeb5023..f6c117cf915 100644 --- a/tools/delly/merge.xml +++ b/tools/delly/merge.xml @@ -1,3 +1,4 @@ + structural variants across/within BCF/VCF file(s) @@ -87,7 +88,7 @@ $generic.pass - + @@ -125,7 +126,7 @@ $generic.pass - + @@ -144,7 +145,7 @@ $generic.pass - + From 8a76dd79f8be36e851a2c4c7989e9ce8b1a943d8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 3 Sep 2024 12:05:50 +0200 Subject: [PATCH 15/15] Update tools/abricate/abricate_list.xml Co-authored-by: M Bernt --- tools/abricate/abricate_list.xml | 1 - 1 file changed, 1 deletion(-) diff --git a/tools/abricate/abricate_list.xml b/tools/abricate/abricate_list.xml index f46514675af..3564cc1a495 100644 --- a/tools/abricate/abricate_list.xml +++ b/tools/abricate/abricate_list.xml @@ -13,7 +13,6 @@ abricate --list > '$report' ]]> -