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/.skip_lint b/data_managers/data_manager_bowtie2_index_builder/.skip_lint new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/data_managers/data_manager_bowtie2_index_builder/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/data_managers/data_manager_bowtie_index_builder/.skip_lint b/data_managers/data_manager_bowtie_index_builder/.skip_lint new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/data_managers/data_manager_bowtie_index_builder/.skip_lint @@ -0,0 +1 @@ +TestsMissing diff --git a/data_managers/data_manager_build_kma_index/.skip_lint b/data_managers/data_manager_build_kma_index/.skip_lint new file mode 100644 index 00000000000..7d044e96aea --- /dev/null +++ b/data_managers/data_manager_build_kma_index/.skip_lint @@ -0,0 +1 @@ +HelpEmpty diff --git a/data_managers/data_manager_build_kraken_database/.skip_lint b/data_managers/data_manager_build_kraken_database/.skip_lint new file mode 100644 index 00000000000..b394139e289 --- /dev/null +++ b/data_managers/data_manager_build_kraken_database/.skip_lint @@ -0,0 +1,2 @@ +HelpEmpty +TestsMissing diff --git a/data_managers/data_manager_bwa_mem_index_builder/.skip_lint b/data_managers/data_manager_bwa_mem_index_builder/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_bwa_mem_index_builder/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_fetch_gene_annotation/.skip_lint b/data_managers/data_manager_fetch_gene_annotation/.skip_lint new file mode 100644 index 00000000000..3e5615e7bb9 --- /dev/null +++ b/data_managers/data_manager_fetch_gene_annotation/.skip_lint @@ -0,0 +1,3 @@ +CitationsMissing +HelpEmpty +TestsMissing diff --git a/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.skip_lint b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_fetch_genome_dbkeys_all_fasta/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_fetch_index_maf/.skip_lint b/data_managers/data_manager_fetch_index_maf/.skip_lint new file mode 100644 index 00000000000..0518d2c178a --- /dev/null +++ b/data_managers/data_manager_fetch_index_maf/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +TestsMissing diff --git a/data_managers/data_manager_fetch_ncbi_taxonomy/.skip_lint b/data_managers/data_manager_fetch_ncbi_taxonomy/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_fetch_ncbi_taxonomy/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_gatk_picard_index_builder/.skip_lint b/data_managers/data_manager_gatk_picard_index_builder/.skip_lint new file mode 100644 index 00000000000..0518d2c178a --- /dev/null +++ b/data_managers/data_manager_gatk_picard_index_builder/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +TestsMissing diff --git a/data_managers/data_manager_genomic_super_signature_ravmodels/.skip_lint b/data_managers/data_manager_genomic_super_signature_ravmodels/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_genomic_super_signature_ravmodels/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_gtdbtk_database_installer/.skip_lint b/data_managers/data_manager_gtdbtk_database_installer/.skip_lint new file mode 100644 index 00000000000..7d044e96aea --- /dev/null +++ b/data_managers/data_manager_gtdbtk_database_installer/.skip_lint @@ -0,0 +1 @@ +HelpEmpty diff --git a/data_managers/data_manager_homer_preparsed/.skip_lint b/data_managers/data_manager_homer_preparsed/.skip_lint new file mode 100644 index 00000000000..a85f2705a91 --- /dev/null +++ b/data_managers/data_manager_homer_preparsed/.skip_lint @@ -0,0 +1,3 @@ +CitationsMissing +HelpEmpty +XMLOrder diff --git a/data_managers/data_manager_kallisto_index_builder/.skip_lint b/data_managers/data_manager_kallisto_index_builder/.skip_lint new file mode 100644 index 00000000000..c779596e7cc --- /dev/null +++ b/data_managers/data_manager_kallisto_index_builder/.skip_lint @@ -0,0 +1,2 @@ +HelpInvalidRST +TestsMissing diff --git a/data_managers/data_manager_malt_index_builder/.skip_lint b/data_managers/data_manager_malt_index_builder/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_malt_index_builder/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_manual/.skip_lint b/data_managers/data_manager_manual/.skip_lint new file mode 100644 index 00000000000..e9fed198f57 --- /dev/null +++ b/data_managers/data_manager_manual/.skip_lint @@ -0,0 +1,3 @@ +CitationsMissing +InputsSelectDynamicOptions +XMLOrder diff --git a/data_managers/data_manager_mash_sketch_builder/.skip_lint b/data_managers/data_manager_mash_sketch_builder/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_mash_sketch_builder/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_mothur_toolsuite/.skip_lint b/data_managers/data_manager_mothur_toolsuite/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_mothur_toolsuite/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_packaged_annotation_data/.skip_lint b/data_managers/data_manager_packaged_annotation_data/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_packaged_annotation_data/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_pangolin_data/.skip_lint b/data_managers/data_manager_pangolin_data/.skip_lint new file mode 100644 index 00000000000..6a91ffad01c --- /dev/null +++ b/data_managers/data_manager_pangolin_data/.skip_lint @@ -0,0 +1,2 @@ +RequirementVersionMissing +XMLOrder diff --git a/data_managers/data_manager_picard_index_builder/.skip_lint b/data_managers/data_manager_picard_index_builder/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_picard_index_builder/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_qiime_database_downloader/.skip_lint b/data_managers/data_manager_qiime_database_downloader/.skip_lint new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/data_managers/data_manager_qiime_database_downloader/.skip_lint @@ -0,0 +1 @@ +TestsMissing diff --git a/data_managers/data_manager_salmon_index_builder/.skip_lint b/data_managers/data_manager_salmon_index_builder/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_salmon_index_builder/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_sam_fasta_index_builder/.skip_lint b/data_managers/data_manager_sam_fasta_index_builder/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/data_managers/data_manager_sam_fasta_index_builder/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/data_managers/data_manager_selection_background/.skip_lint b/data_managers/data_manager_selection_background/.skip_lint new file mode 100644 index 00000000000..d3a1493f388 --- /dev/null +++ b/data_managers/data_manager_selection_background/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +HelpEmpty diff --git a/data_managers/data_manager_semibin/.skip_lint b/data_managers/data_manager_semibin/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/data_managers/data_manager_semibin/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/data_managers/data_manager_snpeff/.skip_lint b/data_managers/data_manager_snpeff/.skip_lint new file mode 100644 index 00000000000..ac58e24884a --- /dev/null +++ b/data_managers/data_manager_snpeff/.skip_lint @@ -0,0 +1,2 @@ +InputsMissing +ToolVersionPEP404 diff --git a/data_managers/data_manager_star_index_builder/.skip_lint b/data_managers/data_manager_star_index_builder/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/data_managers/data_manager_star_index_builder/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/data_managers/data_manager_twobit_builder/.skip_lint b/data_managers/data_manager_twobit_builder/.skip_lint new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/data_managers/data_manager_twobit_builder/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/data_managers/data_manager_vsnp_dnaprints/.skip_lint b/data_managers/data_manager_vsnp_dnaprints/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_dnaprints/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/data_managers/data_manager_vsnp_excel/.skip_lint b/data_managers/data_manager_vsnp_excel/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_excel/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/data_managers/data_manager_vsnp_genbank/.skip_lint b/data_managers/data_manager_vsnp_genbank/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/data_managers/data_manager_vsnp_genbank/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tool_collections/cufflinks/cuffdiff/.skip_lint b/tool_collections/cufflinks/cuffdiff/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tool_collections/cufflinks/cuffdiff/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tool_collections/cufflinks/cuffnorm/.skip_lint b/tool_collections/cufflinks/cuffnorm/.skip_lint new file mode 100644 index 00000000000..db401a876bb --- /dev/null +++ b/tool_collections/cufflinks/cuffnorm/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +OutputsNameDuplicated diff --git a/tool_collections/fastx_toolkit/fastx_clipper/.skip_lint b/tool_collections/fastx_toolkit/fastx_clipper/.skip_lint new file mode 100644 index 00000000000..f1a9e0e1123 --- /dev/null +++ b/tool_collections/fastx_toolkit/fastx_clipper/.skip_lint @@ -0,0 +1 @@ +InputsSelectOptionsDeprecatedAttr diff --git a/tool_collections/galaxy_sequence_utils/fastq_combiner/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_combiner/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_combiner/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_filter/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_filter/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_filter/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_groomer/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_groomer/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_groomer/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_manipulation/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_manipulation/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.skip_lint new file mode 100644 index 00000000000..5a3d475d5d1 --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer/.skip_lint @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_stats/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_stats/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_stats/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_to_tabular/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastq_trimmer/.skip_lint b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastq_trimmer/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/fastqtofasta/.skip_lint b/tool_collections/galaxy_sequence_utils/fastqtofasta/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/fastqtofasta/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.skip_lint b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tool_collections/galaxy_sequence_utils/tabular_to_fastq/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tool_collections/snpeff/.skip_lint b/tool_collections/snpeff/.skip_lint new file mode 100644 index 00000000000..a505b27b40f --- /dev/null +++ b/tool_collections/snpeff/.skip_lint @@ -0,0 +1,3 @@ +InputsDataOptionsFilterAttribFiltersType +InputsDataOptionsFiltersRef +TestsExpectNumOutputs diff --git a/tool_collections/snpsift/snpsift/.skip_lint b/tool_collections/snpsift/snpsift/.skip_lint new file mode 100644 index 00000000000..039bcb6e720 --- /dev/null +++ b/tool_collections/snpsift/snpsift/.skip_lint @@ -0,0 +1,2 @@ +TestsMissing +XMLOrder diff --git a/tool_collections/snpsift/snpsift_dbnsfp/.skip_lint b/tool_collections/snpsift/snpsift_dbnsfp/.skip_lint new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tool_collections/snpsift/snpsift_dbnsfp/.skip_lint @@ -0,0 +1 @@ +TestsMissing diff --git a/tool_collections/snpsift/snpsift_genesets/.skip_lint b/tool_collections/snpsift/snpsift_genesets/.skip_lint new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tool_collections/snpsift/snpsift_genesets/.skip_lint @@ -0,0 +1 @@ +TestsMissing diff --git a/tool_collections/vcflib/vcffilter/.skip_lint b/tool_collections/vcflib/vcffilter/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tool_collections/vcflib/vcffilter/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tool_collections/vcflib/vcfsort/.skip_lint b/tool_collections/vcflib/vcfsort/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tool_collections/vcflib/vcfsort/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/abricate/.skip_lint b/tools/abricate/.skip_lint new file mode 100644 index 00000000000..0332c4d534d --- /dev/null +++ b/tools/abricate/.skip_lint @@ -0,0 +1,2 @@ +InputsMissing +XMLOrder diff --git a/tools/add_input_name_as_column/.skip_lint b/tools/add_input_name_as_column/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/add_input_name_as_column/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/allegro/.skip_lint b/tools/allegro/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/allegro/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/amplican/.skip_lint b/tools/amplican/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/amplican/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/arriba/.skip_lint b/tools/arriba/.skip_lint new file mode 100644 index 00000000000..1d303e867c4 --- /dev/null +++ b/tools/arriba/.skip_lint @@ -0,0 +1 @@ +ValidatorExpression diff --git a/tools/art/.skip_lint b/tools/art/.skip_lint new file mode 100644 index 00000000000..de67bcbc665 --- /dev/null +++ b/tools/art/.skip_lint @@ -0,0 +1,4 @@ +ConditionalParamTypeBool +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/augustus/.skip_lint b/tools/augustus/.skip_lint new file mode 100644 index 00000000000..60dcaf138b5 --- /dev/null +++ b/tools/augustus/.skip_lint @@ -0,0 +1,5 @@ +InputsNameRedundantArgument +InputsSelectOptionDuplicateText +InputsSelectOptionDuplicateValue +TestsExpectNumOutputs +XMLOrder diff --git a/tools/b2btools/.skip_lint b/tools/b2btools/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/b2btools/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/bamutil/.skip_lint b/tools/bamutil/.skip_lint new file mode 100644 index 00000000000..5c3b72bd205 --- /dev/null +++ b/tools/bamutil/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +XMLOrder diff --git a/tools/barcode_splitter/.skip_lint b/tools/barcode_splitter/.skip_lint new file mode 100644 index 00000000000..db6945182f0 --- /dev/null +++ b/tools/barcode_splitter/.skip_lint @@ -0,0 +1,2 @@ +ConditionalWhenMissing +TestsExpectNumOutputs diff --git a/tools/baredsc/.skip_lint b/tools/baredsc/.skip_lint new file mode 100644 index 00000000000..c4bce2614c7 --- /dev/null +++ b/tools/baredsc/.skip_lint @@ -0,0 +1 @@ +EDAMTermsValid diff --git a/tools/barrnap/.skip_lint b/tools/barrnap/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/barrnap/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/bctools/.skip_lint b/tools/bctools/.skip_lint new file mode 100644 index 00000000000..34105185cbe --- /dev/null +++ b/tools/bctools/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +OutputsLabelDuplicatedNoFilter +ToolVersionPEP404 diff --git a/tools/beagle/.skip_lint b/tools/beagle/.skip_lint new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/beagle/.skip_lint @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/bioperl/.skip_lint b/tools/bioperl/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/bioperl/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/blastxml_to_gapped_gff3/.skip_lint b/tools/blastxml_to_gapped_gff3/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/blastxml_to_gapped_gff3/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/bowtie2/.skip_lint b/tools/bowtie2/.skip_lint new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/bowtie2/.skip_lint @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/breseq/.skip_lint b/tools/breseq/.skip_lint new file mode 100644 index 00000000000..d3e0aac05cd --- /dev/null +++ b/tools/breseq/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/bwa/.skip_lint b/tools/bwa/.skip_lint new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/bwa/.skip_lint @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/bwa_mem2/.skip_lint b/tools/bwa_mem2/.skip_lint new file mode 100644 index 00000000000..726b67ea618 --- /dev/null +++ b/tools/bwa_mem2/.skip_lint @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +XMLOrder diff --git a/tools/cat/.skip_lint b/tools/cat/.skip_lint new file mode 100644 index 00000000000..b25348ad77a --- /dev/null +++ b/tools/cat/.skip_lint @@ -0,0 +1,2 @@ +InputsMissing +TestsMissing diff --git a/tools/cdhit/.skip_lint b/tools/cdhit/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/cdhit/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/charts/.skip_lint b/tools/charts/.skip_lint new file mode 100644 index 00000000000..1f14b74af93 --- /dev/null +++ b/tools/charts/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +HelpMissing diff --git a/tools/checkm/.skip_lint b/tools/checkm/.skip_lint new file mode 100644 index 00000000000..db401a876bb --- /dev/null +++ b/tools/checkm/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +OutputsNameDuplicated diff --git a/tools/cherri/.skip_lint b/tools/cherri/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/cherri/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/chira/.skip_lint b/tools/chira/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/chira/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/circexplorer2/.skip_lint b/tools/circexplorer2/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/circexplorer2/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/circos/.skip_lint b/tools/circos/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/circos/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/cite_seq_count/.skip_lint b/tools/cite_seq_count/.skip_lint new file mode 100644 index 00000000000..c4bce2614c7 --- /dev/null +++ b/tools/cite_seq_count/.skip_lint @@ -0,0 +1 @@ +EDAMTermsValid diff --git a/tools/colibread/.skip_lint b/tools/colibread/.skip_lint new file mode 100644 index 00000000000..dd8fa0cea19 --- /dev/null +++ b/tools/colibread/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/collection_column_join/.skip_lint b/tools/collection_column_join/.skip_lint new file mode 100644 index 00000000000..0d0dda5a1ff --- /dev/null +++ b/tools/collection_column_join/.skip_lint @@ -0,0 +1,3 @@ +CitationsNoValid +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/tools/collection_element_identifiers/.skip_lint b/tools/collection_element_identifiers/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/collection_element_identifiers/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/column_maker/.skip_lint b/tools/column_maker/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/column_maker/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/column_order_header_sort/.skip_lint b/tools/column_order_header_sort/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/column_order_header_sort/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/column_remove_by_header/.skip_lint b/tools/column_remove_by_header/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/column_remove_by_header/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/compress_file/.skip_lint b/tools/compress_file/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/compress_file/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/crossmap/.skip_lint b/tools/crossmap/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/crossmap/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/cutesv/.skip_lint b/tools/cutesv/.skip_lint new file mode 100644 index 00000000000..066d952b239 --- /dev/null +++ b/tools/cutesv/.skip_lint @@ -0,0 +1,2 @@ +TestsParamInInputs +XMLOrder diff --git a/tools/cwpair2/.skip_lint b/tools/cwpair2/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/cwpair2/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/decontaminator/.skip_lint b/tools/decontaminator/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/decontaminator/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/deg_annotate/.skip_lint b/tools/deg_annotate/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/deg_annotate/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/delly/.skip_lint b/tools/delly/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/delly/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/diamond/.skip_lint b/tools/diamond/.skip_lint new file mode 100644 index 00000000000..ef8b8e468d5 --- /dev/null +++ b/tools/diamond/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter diff --git a/tools/disco/.skip_lint b/tools/disco/.skip_lint new file mode 100644 index 00000000000..848f337dbe2 --- /dev/null +++ b/tools/disco/.skip_lint @@ -0,0 +1,4 @@ +CitationsNoValid +InputsNameDuplicateOutput +TestsExpectNumOutputs +XMLOrder diff --git a/tools/dnaweaver/.skip_lint b/tools/dnaweaver/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/dnaweaver/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/dropletutils/.skip_lint b/tools/dropletutils/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/dropletutils/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/emboss_5/.skip_lint b/tools/emboss_5/.skip_lint new file mode 100644 index 00000000000..f743e01720f --- /dev/null +++ b/tools/emboss_5/.skip_lint @@ -0,0 +1,6 @@ +InputsSelectOptionDuplicateText +OutputsLabelDuplicatedNoFilter +TestsMissing +TestsParamInInputs +ToolIDWhitespace +XMLOrder diff --git a/tools/exonerate/.skip_lint b/tools/exonerate/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/exonerate/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/extract_genomic_dna/.skip_lint b/tools/extract_genomic_dna/.skip_lint new file mode 100644 index 00000000000..709ca00eeae --- /dev/null +++ b/tools/extract_genomic_dna/.skip_lint @@ -0,0 +1 @@ +ToolIDWhitespace diff --git a/tools/fasta_nucleotide_color_plot/.skip_lint b/tools/fasta_nucleotide_color_plot/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/fasta_nucleotide_color_plot/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/fasttree/.skip_lint b/tools/fasttree/.skip_lint new file mode 100644 index 00000000000..7ed34e66e91 --- /dev/null +++ b/tools/fasttree/.skip_lint @@ -0,0 +1,4 @@ +InputsBoolDistinctValues +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/fermikit/.skip_lint b/tools/fermikit/.skip_lint new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/fermikit/.skip_lint @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/fgsea/.skip_lint b/tools/fgsea/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/fgsea/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/flair/.skip_lint b/tools/flair/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/flair/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/flash/.skip_lint b/tools/flash/.skip_lint new file mode 100644 index 00000000000..3cb4b53ca3f --- /dev/null +++ b/tools/flash/.skip_lint @@ -0,0 +1,4 @@ +InputsBoolDistinctValues +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter +XMLOrder diff --git a/tools/fraggenescan/.skip_lint b/tools/fraggenescan/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/fraggenescan/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/freebayes/.skip_lint b/tools/freebayes/.skip_lint new file mode 100644 index 00000000000..d3e0aac05cd --- /dev/null +++ b/tools/freebayes/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/gatk4/.skip_lint b/tools/gatk4/.skip_lint new file mode 100644 index 00000000000..6eb36d713a8 --- /dev/null +++ b/tools/gatk4/.skip_lint @@ -0,0 +1,5 @@ +InputsNameDuplicate +InputsNameRedundantArgument +TestsExpectNumOutputs +TestsParamInInputs +ToolVersionPEP404 diff --git a/tools/gecko/.skip_lint b/tools/gecko/.skip_lint new file mode 100644 index 00000000000..887ade8ade3 --- /dev/null +++ b/tools/gecko/.skip_lint @@ -0,0 +1 @@ +ConditionalWhenMissing diff --git a/tools/gemini/.skip_lint b/tools/gemini/.skip_lint new file mode 100644 index 00000000000..5bade0f665b --- /dev/null +++ b/tools/gemini/.skip_lint @@ -0,0 +1,5 @@ +InputsDataOptionsFilterAttribFiltersType +InputsDataOptionsFiltersRef +InputsDataOptionsFiltersType +InputsNameRedundantArgument +XMLOrder diff --git a/tools/genehunter_modscore/.skip_lint b/tools/genehunter_modscore/.skip_lint new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/genehunter_modscore/.skip_lint @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/genomic_super_signature/.skip_lint b/tools/genomic_super_signature/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/genomic_super_signature/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/gfa_to_fa/.skip_lint b/tools/gfa_to_fa/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/gfa_to_fa/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/gffcompare/.skip_lint b/tools/gffcompare/.skip_lint new file mode 100644 index 00000000000..7a3c986a235 --- /dev/null +++ b/tools/gffcompare/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +TestsOutputCompareAttrib diff --git a/tools/ggplot2/.skip_lint b/tools/ggplot2/.skip_lint new file mode 100644 index 00000000000..00354267bf3 --- /dev/null +++ b/tools/ggplot2/.skip_lint @@ -0,0 +1,4 @@ +CitationsNoValid +InputsNameDuplicate +TestsExpectNumOutputs +XMLOrder diff --git a/tools/ggupset/.skip_lint b/tools/ggupset/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/ggupset/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/glimmer/.skip_lint b/tools/glimmer/.skip_lint new file mode 100644 index 00000000000..522ad865ff6 --- /dev/null +++ b/tools/glimmer/.skip_lint @@ -0,0 +1,5 @@ +CommandTODO +InputsBoolDistinctValues +OutputsLabelDuplicatedNoFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/goenrichment/.skip_lint b/tools/goenrichment/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/goenrichment/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/goseq/.skip_lint b/tools/goseq/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/goseq/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/gprofiler/.skip_lint b/tools/gprofiler/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/gprofiler/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/gvcftools/.skip_lint b/tools/gvcftools/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/gvcftools/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/hansel/.skip_lint b/tools/hansel/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/hansel/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/happy/.skip_lint b/tools/happy/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/happy/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/hicstuff/.skip_lint b/tools/hicstuff/.skip_lint new file mode 100644 index 00000000000..281a52d416d --- /dev/null +++ b/tools/hicstuff/.skip_lint @@ -0,0 +1 @@ +OutputsLabelDuplicatedNoFilter diff --git a/tools/hisat2/.skip_lint b/tools/hisat2/.skip_lint new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/hisat2/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/hivclustering/.skip_lint b/tools/hivclustering/.skip_lint new file mode 100644 index 00000000000..be639814573 --- /dev/null +++ b/tools/hivclustering/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsParamInInputs diff --git a/tools/hybpiper/.skip_lint b/tools/hybpiper/.skip_lint new file mode 100644 index 00000000000..273da24a36f --- /dev/null +++ b/tools/hybpiper/.skip_lint @@ -0,0 +1 @@ +XSD diff --git a/tools/hyphy/.skip_lint b/tools/hyphy/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/hyphy/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/hypo/.skip_lint b/tools/hypo/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/hypo/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/idba_ud/.skip_lint b/tools/idba_ud/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/idba_ud/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/idr/.skip_lint b/tools/idr/.skip_lint new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/idr/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/idr_download/.skip_lint b/tools/idr_download/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/idr_download/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/iedb_api/.skip_lint b/tools/iedb_api/.skip_lint new file mode 100644 index 00000000000..eb29b9f6a92 --- /dev/null +++ b/tools/iedb_api/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +ValidatorExpressionFuture diff --git a/tools/intermine_galaxy_exchange/.skip_lint b/tools/intermine_galaxy_exchange/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/intermine_galaxy_exchange/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/interproscan/.skip_lint b/tools/interproscan/.skip_lint new file mode 100644 index 00000000000..20069136018 --- /dev/null +++ b/tools/interproscan/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputsFailing +ToolVersionPEP404 diff --git a/tools/intervene/.skip_lint b/tools/intervene/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/intervene/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/iwtomics/.skip_lint b/tools/iwtomics/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/iwtomics/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/jbrowse/.skip_lint b/tools/jbrowse/.skip_lint new file mode 100644 index 00000000000..619947ad80b --- /dev/null +++ b/tools/jbrowse/.skip_lint @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +TestsMissing +XMLOrder diff --git a/tools/jellyfish/.skip_lint b/tools/jellyfish/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/jellyfish/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/join_files_by_id/.skip_lint b/tools/join_files_by_id/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/join_files_by_id/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/jq/.skip_lint b/tools/jq/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/jq/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/jvarkit/.skip_lint b/tools/jvarkit/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/jvarkit/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/kallisto/.skip_lint b/tools/kallisto/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/kallisto/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/khmer/.skip_lint b/tools/khmer/.skip_lint new file mode 100644 index 00000000000..078b2b05611 --- /dev/null +++ b/tools/khmer/.skip_lint @@ -0,0 +1,5 @@ +InputsNameRedundantArgument +OutputsLabelDuplicatedNoFilter +OutputsNameInvalidCheetah +TestsExpectNumOutputs +XMLOrder diff --git a/tools/king/.skip_lint b/tools/king/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/king/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/krakentools/.skip_lint b/tools/krakentools/.skip_lint new file mode 100644 index 00000000000..273da24a36f --- /dev/null +++ b/tools/krakentools/.skip_lint @@ -0,0 +1 @@ +XSD diff --git a/tools/lcrgenie/.skip_lint b/tools/lcrgenie/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/lcrgenie/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/length_and_gc_content/.skip_lint b/tools/length_and_gc_content/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/length_and_gc_content/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/links/.skip_lint b/tools/links/.skip_lint new file mode 100644 index 00000000000..aaf98e466e4 --- /dev/null +++ b/tools/links/.skip_lint @@ -0,0 +1,2 @@ +ToolVersionPEP404 +XMLOrder diff --git a/tools/lofreq/.skip_lint b/tools/lofreq/.skip_lint new file mode 100644 index 00000000000..be639814573 --- /dev/null +++ b/tools/lofreq/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsParamInInputs diff --git a/tools/mageck/.skip_lint b/tools/mageck/.skip_lint new file mode 100644 index 00000000000..d3e0aac05cd --- /dev/null +++ b/tools/mageck/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/maker/.skip_lint b/tools/maker/.skip_lint new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/maker/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/malt/.skip_lint b/tools/malt/.skip_lint new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/malt/.skip_lint @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/map_param_value/.skip_lint b/tools/map_param_value/.skip_lint new file mode 100644 index 00000000000..52d545dc64f --- /dev/null +++ b/tools/map_param_value/.skip_lint @@ -0,0 +1 @@ +InputsDataFormat diff --git a/tools/mash/.skip_lint b/tools/mash/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/mash/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/masigpro/.skip_lint b/tools/masigpro/.skip_lint new file mode 100644 index 00000000000..eb2cdb1921c --- /dev/null +++ b/tools/masigpro/.skip_lint @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs diff --git a/tools/megahit_contig2fastg/.skip_lint b/tools/megahit_contig2fastg/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/megahit_contig2fastg/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/megan/.skip_lint b/tools/megan/.skip_lint new file mode 100644 index 00000000000..17796d16c43 --- /dev/null +++ b/tools/megan/.skip_lint @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +InputsNameRedundantArgument diff --git a/tools/meme/.skip_lint b/tools/meme/.skip_lint new file mode 100644 index 00000000000..d3e0aac05cd --- /dev/null +++ b/tools/meme/.skip_lint @@ -0,0 +1,3 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs +XMLOrder diff --git a/tools/merlin/.skip_lint b/tools/merlin/.skip_lint new file mode 100644 index 00000000000..281a52d416d --- /dev/null +++ b/tools/merlin/.skip_lint @@ -0,0 +1 @@ +OutputsLabelDuplicatedNoFilter diff --git a/tools/metaeuk/.skip_lint b/tools/metaeuk/.skip_lint new file mode 100644 index 00000000000..02cd7e2bd7e --- /dev/null +++ b/tools/metaeuk/.skip_lint @@ -0,0 +1,4 @@ +InputsNameRedundantArgument +OutputsLabelDuplicatedNoFilter +ToolVersionPEP404 +XMLOrder diff --git a/tools/metagenomeseq/.skip_lint b/tools/metagenomeseq/.skip_lint new file mode 100644 index 00000000000..005c9030cff --- /dev/null +++ b/tools/metagenomeseq/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +ToolVersionPEP404 diff --git a/tools/migmap/.skip_lint b/tools/migmap/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/migmap/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/minia/.skip_lint b/tools/minia/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/minia/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/mirnature/.skip_lint b/tools/mirnature/.skip_lint new file mode 100644 index 00000000000..561ac4b4543 --- /dev/null +++ b/tools/mirnature/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/tools/mlst/.skip_lint b/tools/mlst/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/mlst/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/moabs/.skip_lint b/tools/moabs/.skip_lint new file mode 100644 index 00000000000..887ade8ade3 --- /dev/null +++ b/tools/moabs/.skip_lint @@ -0,0 +1 @@ +ConditionalWhenMissing diff --git a/tools/mothur/.skip_lint b/tools/mothur/.skip_lint new file mode 100644 index 00000000000..c538ac8fe2f --- /dev/null +++ b/tools/mothur/.skip_lint @@ -0,0 +1,5 @@ +HelpInvalidRST +OutputsLabelDuplicatedFilter +OutputsNameInvalidCheetah +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/msaboot/.skip_lint b/tools/msaboot/.skip_lint new file mode 100644 index 00000000000..c40bf0a2782 --- /dev/null +++ b/tools/msaboot/.skip_lint @@ -0,0 +1,2 @@ +InputsBoolDistinctValues +TestsExpectNumOutputs diff --git a/tools/multigps/.skip_lint b/tools/multigps/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/multigps/.skip_lint @@ -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/.skip_lint b/tools/mykrobe/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/mykrobe/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/mzmine/.skip_lint b/tools/mzmine/.skip_lint new file mode 100644 index 00000000000..fd9005475bf --- /dev/null +++ b/tools/mzmine/.skip_lint @@ -0,0 +1 @@ +TestsMissing diff --git a/tools/naltorfs/.skip_lint b/tools/naltorfs/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/naltorfs/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/nanocompore/.skip_lint b/tools/nanocompore/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/nanocompore/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ncbi_acc_download/.skip_lint b/tools/ncbi_acc_download/.skip_lint new file mode 100644 index 00000000000..8300ec2e860 --- /dev/null +++ b/tools/ncbi_acc_download/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputs diff --git a/tools/ncbi_entrez_eutils/.skip_lint b/tools/ncbi_entrez_eutils/.skip_lint new file mode 100644 index 00000000000..8fac1952a0d --- /dev/null +++ b/tools/ncbi_entrez_eutils/.skip_lint @@ -0,0 +1,2 @@ +InputsNameDuplicate +TestsExpectNumOutputs diff --git a/tools/necat/.skip_lint b/tools/necat/.skip_lint new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/necat/.skip_lint @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/newick_utils/.skip_lint b/tools/newick_utils/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/newick_utils/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ngmlr/.skip_lint b/tools/ngmlr/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/ngmlr/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ngsutils/.skip_lint b/tools/ngsutils/.skip_lint new file mode 100644 index 00000000000..855dee9e6e0 --- /dev/null +++ b/tools/ngsutils/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +XMLOrder diff --git a/tools/ococo/.skip_lint b/tools/ococo/.skip_lint new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/ococo/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/odgi/.skip_lint b/tools/odgi/.skip_lint new file mode 100644 index 00000000000..8300ec2e860 --- /dev/null +++ b/tools/odgi/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputs diff --git a/tools/packaged_annotation_loader/.skip_lint b/tools/packaged_annotation_loader/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/packaged_annotation_loader/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/pathview/.skip_lint b/tools/pathview/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/pathview/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/pbgcpp/.skip_lint b/tools/pbgcpp/.skip_lint new file mode 100644 index 00000000000..9c757f1de60 --- /dev/null +++ b/tools/pbgcpp/.skip_lint @@ -0,0 +1,2 @@ +CitationsMissing +TestsExpectNumOutputs diff --git a/tools/pe_histogram/.skip_lint b/tools/pe_histogram/.skip_lint new file mode 100644 index 00000000000..281a52d416d --- /dev/null +++ b/tools/pe_histogram/.skip_lint @@ -0,0 +1 @@ +OutputsLabelDuplicatedNoFilter diff --git a/tools/picard/.skip_lint b/tools/picard/.skip_lint new file mode 100644 index 00000000000..5e180cb3ab4 --- /dev/null +++ b/tools/picard/.skip_lint @@ -0,0 +1 @@ +ConditionalParamTypeBool diff --git a/tools/picrust2/.skip_lint b/tools/picrust2/.skip_lint new file mode 100644 index 00000000000..208f465e2bc --- /dev/null +++ b/tools/picrust2/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputsFailing diff --git a/tools/pilon/.skip_lint b/tools/pilon/.skip_lint new file mode 100644 index 00000000000..eb2cdb1921c --- /dev/null +++ b/tools/pilon/.skip_lint @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs diff --git a/tools/pizzly/.skip_lint b/tools/pizzly/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/pizzly/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/plink/.skip_lint b/tools/plink/.skip_lint new file mode 100644 index 00000000000..d710671f533 --- /dev/null +++ b/tools/plink/.skip_lint @@ -0,0 +1 @@ +ToolVersionPEP404 diff --git a/tools/porechop/.skip_lint b/tools/porechop/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/porechop/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/poretools/.skip_lint b/tools/poretools/.skip_lint new file mode 100644 index 00000000000..37306aaf5f8 --- /dev/null +++ b/tools/poretools/.skip_lint @@ -0,0 +1,7 @@ +InputsNameDuplicate +InputsNameRedundantArgument +InputsSelectOptionDuplicateText +InputsSelectOptionDuplicateValue +TestsParamInInputs +ToolVersionPEP404 +XMLOrder diff --git a/tools/presto/.skip_lint b/tools/presto/.skip_lint new file mode 100644 index 00000000000..88c3f1f4ea1 --- /dev/null +++ b/tools/presto/.skip_lint @@ -0,0 +1,4 @@ +OutputsLabelDuplicatedFilter +OutputsLabelDuplicatedNoFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/prinseq/.skip_lint b/tools/prinseq/.skip_lint new file mode 100644 index 00000000000..5c3b72bd205 --- /dev/null +++ b/tools/prinseq/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +XMLOrder diff --git a/tools/progressivemauve/.skip_lint b/tools/progressivemauve/.skip_lint new file mode 100644 index 00000000000..f885163c07d --- /dev/null +++ b/tools/progressivemauve/.skip_lint @@ -0,0 +1,3 @@ +CitationsNoValid +HelpInvalidRST +ToolVersionPEP404 diff --git a/tools/prokka/.skip_lint b/tools/prokka/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/prokka/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/pureclip/.skip_lint b/tools/pureclip/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/pureclip/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/quickmerge/.skip_lint b/tools/quickmerge/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/quickmerge/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/raceid/.skip_lint b/tools/raceid/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/raceid/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rapidnj/.skip_lint b/tools/rapidnj/.skip_lint new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/rapidnj/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/rcorrector/.skip_lint b/tools/rcorrector/.skip_lint new file mode 100644 index 00000000000..eb2cdb1921c --- /dev/null +++ b/tools/rcorrector/.skip_lint @@ -0,0 +1,2 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs diff --git a/tools/repeatmasker/.skip_lint b/tools/repeatmasker/.skip_lint new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/repeatmasker/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/repmatch_gff3/.skip_lint b/tools/repmatch_gff3/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/repmatch_gff3/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/ribowaltz/.skip_lint b/tools/ribowaltz/.skip_lint new file mode 100644 index 00000000000..c4bce2614c7 --- /dev/null +++ b/tools/ribowaltz/.skip_lint @@ -0,0 +1 @@ +EDAMTermsValid diff --git a/tools/roary/.skip_lint b/tools/roary/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/roary/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rp2biosensor/.skip_lint b/tools/rp2biosensor/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/rp2biosensor/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/rptools/.skip_lint b/tools/rptools/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/rptools/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/rrparser/.skip_lint b/tools/rrparser/.skip_lint new file mode 100644 index 00000000000..887ade8ade3 --- /dev/null +++ b/tools/rrparser/.skip_lint @@ -0,0 +1 @@ +ConditionalWhenMissing diff --git a/tools/ruvseq/.skip_lint b/tools/ruvseq/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/ruvseq/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/salsa2/.skip_lint b/tools/salsa2/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/salsa2/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/samblaster/.skip_lint b/tools/samblaster/.skip_lint new file mode 100644 index 00000000000..44e038a095b --- /dev/null +++ b/tools/samblaster/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +TestsParamInInputs diff --git a/tools/sbml2sbol/.skip_lint b/tools/sbml2sbol/.skip_lint new file mode 100644 index 00000000000..46f5e08e85b --- /dev/null +++ b/tools/sbml2sbol/.skip_lint @@ -0,0 +1 @@ +CitationsMissing diff --git a/tools/scater/.skip_lint b/tools/scater/.skip_lint new file mode 100644 index 00000000000..9b777a1b5b6 --- /dev/null +++ b/tools/scater/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +XMLOrder diff --git a/tools/scpipe/.skip_lint b/tools/scpipe/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/scpipe/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/seqcomplexity/.skip_lint b/tools/seqcomplexity/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/seqcomplexity/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/seqwish/.skip_lint b/tools/seqwish/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/seqwish/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/shorah/.skip_lint b/tools/shorah/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/shorah/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/sickle/.skip_lint b/tools/sickle/.skip_lint new file mode 100644 index 00000000000..561ac4b4543 --- /dev/null +++ b/tools/sickle/.skip_lint @@ -0,0 +1,2 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs diff --git a/tools/simtext/.skip_lint b/tools/simtext/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/simtext/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/sina/.skip_lint b/tools/sina/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/sina/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/slamdunk/.skip_lint b/tools/slamdunk/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/slamdunk/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/snap/.skip_lint b/tools/snap/.skip_lint new file mode 100644 index 00000000000..aff5d391aff --- /dev/null +++ b/tools/snap/.skip_lint @@ -0,0 +1,3 @@ +CitationsNoValid +ToolVersionPEP404 +XMLOrder diff --git a/tools/sniffles/.skip_lint b/tools/sniffles/.skip_lint new file mode 100644 index 00000000000..066d952b239 --- /dev/null +++ b/tools/sniffles/.skip_lint @@ -0,0 +1,2 @@ +TestsParamInInputs +XMLOrder diff --git a/tools/snippy/.skip_lint b/tools/snippy/.skip_lint new file mode 100644 index 00000000000..e6389d1e57b --- /dev/null +++ b/tools/snippy/.skip_lint @@ -0,0 +1,3 @@ +ConditionalParamTypeBool +TestsExpectNumOutputs +XMLOrder diff --git a/tools/snp-dists/.skip_lint b/tools/snp-dists/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/snp-dists/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/snpeff-covid19/.skip_lint b/tools/snpeff-covid19/.skip_lint new file mode 100644 index 00000000000..38682cfa50a --- /dev/null +++ b/tools/snpeff-covid19/.skip_lint @@ -0,0 +1,3 @@ +TestsExpectNumOutputs +ToolVersionPEP404 +XMLOrder diff --git a/tools/snpfreqplot/.skip_lint b/tools/snpfreqplot/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/snpfreqplot/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/spaln/.skip_lint b/tools/spaln/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/spaln/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/spotyping/.skip_lint b/tools/spotyping/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/spotyping/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/stacks/.skip_lint b/tools/stacks/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/stacks/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/stacks2/.skip_lint b/tools/stacks2/.skip_lint new file mode 100644 index 00000000000..3f36fbca6c2 --- /dev/null +++ b/tools/stacks2/.skip_lint @@ -0,0 +1,3 @@ +CommandTODO +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter diff --git a/tools/star_fusion/.skip_lint b/tools/star_fusion/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/star_fusion/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/strelka/.skip_lint b/tools/strelka/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/strelka/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/structure/.skip_lint b/tools/structure/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/structure/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/structureharvester/.skip_lint b/tools/structureharvester/.skip_lint new file mode 100644 index 00000000000..4d97c7e23e6 --- /dev/null +++ b/tools/structureharvester/.skip_lint @@ -0,0 +1,2 @@ +InputsNameDuplicateOutput +TestsExpectNumOutputs diff --git a/tools/swift/.skip_lint b/tools/swift/.skip_lint new file mode 100644 index 00000000000..c4d48dac9f2 --- /dev/null +++ b/tools/swift/.skip_lint @@ -0,0 +1,2 @@ +InputsNameRedundantArgument +TestsExpectNumOutputs diff --git a/tools/table_compute/.skip_lint b/tools/table_compute/.skip_lint new file mode 100644 index 00000000000..b5212db9362 --- /dev/null +++ b/tools/table_compute/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +TestsExpectNumOutputsFailing diff --git a/tools/tag_pileup_frequency/.skip_lint b/tools/tag_pileup_frequency/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tag_pileup_frequency/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tasmanian_mismatch/.skip_lint b/tools/tasmanian_mismatch/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tasmanian_mismatch/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tbl2gff3/.skip_lint b/tools/tbl2gff3/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/tbl2gff3/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid diff --git a/tools/telescope/.skip_lint b/tools/telescope/.skip_lint new file mode 100644 index 00000000000..5a3d475d5d1 --- /dev/null +++ b/tools/telescope/.skip_lint @@ -0,0 +1,3 @@ +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +XMLOrder diff --git a/tools/tetyper/.skip_lint b/tools/tetyper/.skip_lint new file mode 100644 index 00000000000..cc60dd28c7b --- /dev/null +++ b/tools/tetyper/.skip_lint @@ -0,0 +1 @@ +TestsExpectNumOutputs diff --git a/tools/tn93/.skip_lint b/tools/tn93/.skip_lint new file mode 100644 index 00000000000..232ad9b2230 --- /dev/null +++ b/tools/tn93/.skip_lint @@ -0,0 +1,2 @@ +HelpInvalidRST +OutputsLabelDuplicatedFilter diff --git a/tools/transdecoder/.skip_lint b/tools/transdecoder/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/transdecoder/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/transit/.skip_lint b/tools/transit/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/transit/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/trinotate/.skip_lint b/tools/trinotate/.skip_lint new file mode 100644 index 00000000000..ee3065a51c9 --- /dev/null +++ b/tools/trinotate/.skip_lint @@ -0,0 +1,2 @@ +TestsExpectNumOutputs +XMLOrder diff --git a/tools/tsne/.skip_lint b/tools/tsne/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/tsne/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/tximport/.skip_lint b/tools/tximport/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/tximport/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/ucsc_blat/.skip_lint b/tools/ucsc_blat/.skip_lint new file mode 100644 index 00000000000..a1cf37844af --- /dev/null +++ b/tools/ucsc_blat/.skip_lint @@ -0,0 +1 @@ +TestsOutputCompareAttrib diff --git a/tools/ucsc_tools/fasplit/.skip_lint b/tools/ucsc_tools/fasplit/.skip_lint new file mode 100644 index 00000000000..af4cf5ec3d4 --- /dev/null +++ b/tools/ucsc_tools/fasplit/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +XMLOrder diff --git a/tools/ucsc_tools/twobittofa/.skip_lint b/tools/ucsc_tools/twobittofa/.skip_lint new file mode 100644 index 00000000000..af4cf5ec3d4 --- /dev/null +++ b/tools/ucsc_tools/twobittofa/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +XMLOrder diff --git a/tools/umi_tools/.skip_lint b/tools/umi_tools/.skip_lint new file mode 100644 index 00000000000..dc4adbb445e --- /dev/null +++ b/tools/umi_tools/.skip_lint @@ -0,0 +1,6 @@ +CommandTODO +InputsNameRedundantArgument +OutputsLabelDuplicatedFilter +TestsExpectNumOutputs +TestsParamInInputs +XMLOrder diff --git a/tools/varscan/.skip_lint b/tools/varscan/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/varscan/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/vcf2maf/.skip_lint b/tools/vcf2maf/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/vcf2maf/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/velvet/.skip_lint b/tools/velvet/.skip_lint new file mode 100644 index 00000000000..a68d017209e --- /dev/null +++ b/tools/velvet/.skip_lint @@ -0,0 +1 @@ +XMLOrder diff --git a/tools/vg/.skip_lint b/tools/vg/.skip_lint new file mode 100644 index 00000000000..02e7f1dcf79 --- /dev/null +++ b/tools/vg/.skip_lint @@ -0,0 +1,2 @@ +CitationsNoValid +HelpInvalidRST diff --git a/tools/vsearch/.skip_lint b/tools/vsearch/.skip_lint new file mode 100644 index 00000000000..de4e58e9ed1 --- /dev/null +++ b/tools/vsearch/.skip_lint @@ -0,0 +1,3 @@ +InputsSelectOptionDuplicateText +TestsExpectNumOutputs +XMLOrder diff --git a/tools/vsnp/.skip_lint b/tools/vsnp/.skip_lint new file mode 100644 index 00000000000..dabcb8dc984 --- /dev/null +++ b/tools/vsnp/.skip_lint @@ -0,0 +1 @@ +TestsParamInInputs diff --git a/tools/winnowmap/.skip_lint b/tools/winnowmap/.skip_lint new file mode 100644 index 00000000000..e7d00398ee9 --- /dev/null +++ b/tools/winnowmap/.skip_lint @@ -0,0 +1 @@ +InputsNameRedundantArgument diff --git a/tools/xpath/.skip_lint b/tools/xpath/.skip_lint new file mode 100644 index 00000000000..f98c941cb66 --- /dev/null +++ b/tools/xpath/.skip_lint @@ -0,0 +1 @@ +CitationsNoValid